[Thu Apr 24 13:01:32 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/molecularBarcodeTest.17483480952940654878.sam --RUN_BARCODE HiMom --SAMPLE_ALIAS HiDad --LIBRARY_NAME Hello, World --SEQUENCING_CENTER BI --SORT false --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25S8S25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --PLATFORM ILLUMINA --INCLUDE_BC_IN_RG_TAG false --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:32 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:01:32 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S8S25T
[Thu Apr 24 13:01:32 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:32 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/molecularBarcodeTest.12548315980655798262.sam --RUN_BARCODE HiMom --SAMPLE_ALIAS HiDad --LIBRARY_NAME Hello, World --SEQUENCING_CENTER BI --SORT false --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25S8S25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --PLATFORM ILLUMINA --INCLUDE_BC_IN_RG_TAG false --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:32 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:01:32 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S8S25T
[Thu Apr 24 13:01:32 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:32 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/molecularBarcodeTest.13246823313580795557.sam --RUN_BARCODE HiMom --SAMPLE_ALIAS HiDad --LIBRARY_NAME Hello, World --SEQUENCING_CENTER BI --SORT true --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25S8S25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --PLATFORM ILLUMINA --INCLUDE_BC_IN_RG_TAG false --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:32 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:01:32 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S8S25T
INFO 2025-04-24 13:01:32 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:01:32 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:01:32 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:01:32 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:01:32 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:01:32 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:01:32 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:01:33 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:01:33 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:33 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/molecularBarcodeTest.6844176239007430829.sam --RUN_BARCODE HiMom --SAMPLE_ALIAS HiDad --LIBRARY_NAME Hello, World --SEQUENCING_CENTER BI --SORT true --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25S8S25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --PLATFORM ILLUMINA --INCLUDE_BC_IN_RG_TAG false --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:33 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:01:33 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S8S25T
INFO 2025-04-24 13:01:33 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:01:33 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:01:33 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:01:33 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:01:33 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:01:33 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:01:33 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:01:33 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:01:33 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:33 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/molecularBarcodeTest.5341866202104383343.sam --RUN_BARCODE HiMom --SAMPLE_ALIAS HiDad --LIBRARY_NAME Hello, World --SEQUENCING_CENTER BI --SORT false --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25S8M25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --PLATFORM ILLUMINA --INCLUDE_BC_IN_RG_TAG false --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:33 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:01:33 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S8M25T
[Thu Apr 24 13:01:33 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:33 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/molecularBarcodeTest.16142096432801705418.sam --RUN_BARCODE HiMom --SAMPLE_ALIAS HiDad --LIBRARY_NAME Hello, World --SEQUENCING_CENTER BI --SORT false --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25S8M25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --PLATFORM ILLUMINA --INCLUDE_BC_IN_RG_TAG false --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:33 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:01:33 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S8M25T
[Thu Apr 24 13:01:33 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:33 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/molecularBarcodeTest.13240626112922371218.sam --RUN_BARCODE HiMom --SAMPLE_ALIAS HiDad --LIBRARY_NAME Hello, World --SEQUENCING_CENTER BI --SORT true --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25S8M25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --PLATFORM ILLUMINA --INCLUDE_BC_IN_RG_TAG false --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:33 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:01:33 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S8M25T
INFO 2025-04-24 13:01:33 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:01:33 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:01:33 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:01:33 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:01:33 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:01:33 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:01:33 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:01:33 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:01:33 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:33 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/molecularBarcodeTest.2065253376879552667.sam --RUN_BARCODE HiMom --SAMPLE_ALIAS HiDad --LIBRARY_NAME Hello, World --SEQUENCING_CENTER BI --SORT true --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25S8M25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --PLATFORM ILLUMINA --INCLUDE_BC_IN_RG_TAG false --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:33 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:01:34 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S8M25T
INFO 2025-04-24 13:01:34 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:01:34 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:01:34 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:01:34 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:01:34 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:01:34 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:01:34 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:01:34 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:01:34 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:34 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/molecularBarcodeTest.6857671179967157719.sam --RUN_BARCODE HiMom --SAMPLE_ALIAS HiDad --LIBRARY_NAME Hello, World --SEQUENCING_CENTER BI --SORT false --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25S8M25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --PLATFORM ILLUMINA --INCLUDE_BC_IN_RG_TAG false --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:34 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:01:34 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S8M25T
[Thu Apr 24 13:01:34 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:34 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/molecularBarcodeTest.18431439683958618276.sam --RUN_BARCODE HiMom --SAMPLE_ALIAS HiDad --LIBRARY_NAME Hello, World --SEQUENCING_CENTER BI --SORT false --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25S8M25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --PLATFORM ILLUMINA --INCLUDE_BC_IN_RG_TAG false --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:34 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:01:34 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S8M25T
[Thu Apr 24 13:01:34 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:34 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/molecularBarcodeTest.339812378661973303.sam --RUN_BARCODE HiMom --SAMPLE_ALIAS HiDad --LIBRARY_NAME Hello, World --SEQUENCING_CENTER BI --SORT true --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25S8M25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --PLATFORM ILLUMINA --INCLUDE_BC_IN_RG_TAG false --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:34 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:01:34 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S8M25T
INFO 2025-04-24 13:01:34 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:01:34 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:01:34 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:01:34 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:01:34 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:01:34 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:01:34 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:01:34 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:01:34 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:34 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/molecularBarcodeTest.17551605207114145549.sam --RUN_BARCODE HiMom --SAMPLE_ALIAS HiDad --LIBRARY_NAME Hello, World --SEQUENCING_CENTER BI --SORT true --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25S8M25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --PLATFORM ILLUMINA --INCLUDE_BC_IN_RG_TAG false --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:34 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:01:34 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S8M25T
INFO 2025-04-24 13:01:34 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:01:34 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:01:34 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:01:35 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:01:35 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:01:35 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:01:35 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:01:35 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:01:35 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:35 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/molecularBarcodeTest.11269449090406104993.sam --RUN_BARCODE HiMom --SAMPLE_ALIAS HiDad --LIBRARY_NAME Hello, World --SEQUENCING_CENTER BI --SORT false --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25S4M4M25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --PLATFORM ILLUMINA --INCLUDE_BC_IN_RG_TAG false --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:35 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:01:35 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S4M4M25T
[Thu Apr 24 13:01:35 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:35 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/molecularBarcodeTest.16410928669597166472.sam --RUN_BARCODE HiMom --SAMPLE_ALIAS HiDad --LIBRARY_NAME Hello, World --SEQUENCING_CENTER BI --SORT false --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25S4M4M25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --PLATFORM ILLUMINA --INCLUDE_BC_IN_RG_TAG false --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:35 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:01:35 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S4M4M25T
[Thu Apr 24 13:01:35 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:35 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/molecularBarcodeTest.6990757048048488944.sam --RUN_BARCODE HiMom --SAMPLE_ALIAS HiDad --LIBRARY_NAME Hello, World --SEQUENCING_CENTER BI --SORT true --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25S4M4M25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --PLATFORM ILLUMINA --INCLUDE_BC_IN_RG_TAG false --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:35 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:01:35 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S4M4M25T
INFO 2025-04-24 13:01:35 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:01:35 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:01:35 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:01:35 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:01:35 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:01:35 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:01:35 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:01:35 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:01:35 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:35 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/molecularBarcodeTest.16515174790696293119.sam --RUN_BARCODE HiMom --SAMPLE_ALIAS HiDad --LIBRARY_NAME Hello, World --SEQUENCING_CENTER BI --SORT true --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25S4M4M25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --PLATFORM ILLUMINA --INCLUDE_BC_IN_RG_TAG false --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:35 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:01:35 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S4M4M25T
INFO 2025-04-24 13:01:35 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:01:35 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:01:35 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:01:36 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:01:36 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:01:36 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:01:36 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:01:36 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:01:36 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:36 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/molecularBarcodeTest.11864352176695994117.sam --RUN_BARCODE HiMom --SAMPLE_ALIAS HiDad --LIBRARY_NAME Hello, World --SEQUENCING_CENTER BI --TAG_PER_MOLECULAR_INDEX ZA --TAG_PER_MOLECULAR_INDEX ZB --SORT false --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25S4M4M25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --PLATFORM ILLUMINA --INCLUDE_BC_IN_RG_TAG false --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:36 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:01:36 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S4M4M25T
[Thu Apr 24 13:01:36 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:36 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/molecularBarcodeTest.14286685816465417017.sam --RUN_BARCODE HiMom --SAMPLE_ALIAS HiDad --LIBRARY_NAME Hello, World --SEQUENCING_CENTER BI --TAG_PER_MOLECULAR_INDEX ZA --TAG_PER_MOLECULAR_INDEX ZB --SORT false --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25S4M4M25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --PLATFORM ILLUMINA --INCLUDE_BC_IN_RG_TAG false --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:36 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:01:36 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S4M4M25T
[Thu Apr 24 13:01:36 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:36 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/molecularBarcodeTest.13119027526400997435.sam --RUN_BARCODE HiMom --SAMPLE_ALIAS HiDad --LIBRARY_NAME Hello, World --SEQUENCING_CENTER BI --TAG_PER_MOLECULAR_INDEX ZA --TAG_PER_MOLECULAR_INDEX ZB --SORT true --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25S4M4M25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --PLATFORM ILLUMINA --INCLUDE_BC_IN_RG_TAG false --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:36 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:01:36 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S4M4M25T
INFO 2025-04-24 13:01:36 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:01:36 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:01:36 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:01:36 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:01:36 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:01:36 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:01:36 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:01:36 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:01:36 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:36 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/molecularBarcodeTest.8841842004827050249.sam --RUN_BARCODE HiMom --SAMPLE_ALIAS HiDad --LIBRARY_NAME Hello, World --SEQUENCING_CENTER BI --TAG_PER_MOLECULAR_INDEX ZA --TAG_PER_MOLECULAR_INDEX ZB --SORT true --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25S4M4M25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --PLATFORM ILLUMINA --INCLUDE_BC_IN_RG_TAG false --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:36 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:01:36 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S4M4M25T
INFO 2025-04-24 13:01:36 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:01:36 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:01:36 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:01:37 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:01:37 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:01:37 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:01:37 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:01:37 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:01:37 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824
USAGE: IlluminaBasecallsToSam [arguments]
Transforms raw Illumina sequencing data into an unmapped SAM, BAM or CRAM file.<p>The IlluminaBaseCallsToSam program
collects, demultiplexes, and sorts reads across all of the tiles of a lane via barcode to produce an unmapped SAM, BAM
or CRAM file. An unmapped BAM file is often referred to as a uBAM. All barcode, sample, and library data is provided
in the LIBRARY_PARAMS file. Note, this LIBRARY_PARAMS file should be formatted according to the specifications
indicated below. The following is an example of a properly formatted LIBRARY_PARAMS
file:</p>BARCODE_1 OUTPUT SAMPLE_ALIAS LIBRARY_NAME
AAAAAAAA SA_AAAAAAAA.bam SA_AAAAAAAA LN_AAAAAAAA
AAAAGAAG SA_AAAAGAAG.bam SA_AAAAGAAG LN_AAAAGAAG
AACAATGG SA_AACAATGG.bam SA_AACAATGG LN_AACAATGG
N SA_non_indexed.bam SA_non_indexed LN_NNNNNNNN
<p>The BARCODES_DIR file is produced by the <a
href='http://broadinstitute.github.io/picard/command-line-overview.html#ExtractIlluminaBarcodes'>ExtractIlluminaBarcodes</a>
tool for each lane of a flow cell.</p> <p>Barcode matching can be done inline without requiring barcodes files
generated by `ExtractIlluminaBarcode`. By setting MATCH_BARCODES_INLINE to true barcodes will be matched as they are
parsed and converted. Thisdoes not require BARCODES_DIR.</p> <h4>Usage example:</h4><pre>java -jar picard.jar
IlluminaBasecallsToSam \<br /> BASECALLS_DIR=/BaseCalls/ \<br /> LANE=001 \<br /> READ_STRUCTURE=25T8B25T
\<br /> RUN_BARCODE=run15 \<br /> IGNORE_UNEXPECTED_BARCODES=true \<br /> LIBRARY_PARAMS=library.params
</pre><hr />
Version:null
Required Arguments:
--BARCODE_PARAMS <File> Deprecated (use LIBRARY_PARAMS). Tab-separated file for creating all output SAM, BAM or
CRAM files for barcoded run with single IlluminaBasecallsToSam invocation. Columns are
BARCODE, OUTPUT, SAMPLE_ALIAS, and LIBRARY_NAME. Row with BARCODE=N is used to specify a
file for no barcode match Required. Cannot be used in conjunction with argument(s)
OUTPUT (O) SAMPLE_ALIAS (ALIAS) LIBRARY_NAME (LIB) LIBRARY_PARAMS
--BASECALLS_DIR,-B <File> The Illumina basecalls directory. Required.
--LANE,-L <Integer> Lane number. This can be specified multiple times. Reads with the same index in multiple
lanes will be added to the same output file. This argument must be specified at least
once. Required.
--LIBRARY_PARAMS <File> Tab-separated file for creating all output SAM, BAM or CRAM files for a lane with single
IlluminaBasecallsToSam invocation. The columns are OUTPUT, SAMPLE_ALIAS, and
LIBRARY_NAME, BARCODE_1, BARCODE_2 ... BARCODE_X where X = number of barcodes per cluster
(optional). Row with BARCODE_1 set to 'N' is used to specify a file for no barcode match.
You may also provide any 2 letter RG header attributes (excluding PU, CN, PL, and DT) as
columns in this file and the values for those columns will be inserted into the RG tag for
the SAM, BAM or CRAM file created for a given row. Required. Cannot be used in
conjunction with argument(s) OUTPUT (O) SAMPLE_ALIAS (ALIAS) LIBRARY_NAME (LIB)
BARCODE_PARAMS
--OUTPUT,-O <File> Deprecated (use LIBRARY_PARAMS). The output SAM, BAM or CRAM file. Format is determined
by extension. Required. Cannot be used in conjunction with argument(s) BARCODE_PARAMS
LIBRARY_PARAMS
--READ_STRUCTURE,-RS <String> A description of the logical structure of clusters in an Illumina Run, i.e. a description
of the structure IlluminaBasecallsToSam assumes the data to be in. It should consist of
integer/character pairs describing the number of cycles and the type of those cycles (B
for Sample Barcode, M for molecular barcode, T for Template, and S for skip). E.g. If the
input data consists of 80 base clusters and we provide a read structure of "28T8M8B8S28T"
then the sequence may be split up into four reads:
* read one with 28 cycles (bases) of template
* read two with 8 cycles (bases) of molecular barcode (ex. unique molecular barcode)
* read three with 8 cycles (bases) of sample barcode
* 8 cycles (bases) skipped.
* read four with 28 cycles (bases) of template
The skipped cycles would NOT be included in an output SAM/BAM file or in read groups
therein. Required.
--RUN_BARCODE <String> The barcode of the run. Prefixed to read names. Required.
--SAMPLE_ALIAS,-ALIAS <String>Deprecated (use LIBRARY_PARAMS). The name of the sequenced sample Required. Cannot be
used in conjunction with argument(s) BARCODE_PARAMS LIBRARY_PARAMS
--SEQUENCING_CENTER <String> The name of the sequencing center that produced the reads. Used to set the @RG->CN header
tag. Required.
Optional Arguments:
--ADAPTERS_TO_CHECK <IlluminaAdapterPair>
Which adapters to look for in the read. This argument may be specified 0 or more times.
Default value: [INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM]. Possible values:
{PAIRED_END, INDEXED, SINGLE_END, NEXTERA_V1, NEXTERA_V2, DUAL_INDEXED, FLUIDIGM,
TRUSEQ_SMALLRNA, ALTERNATIVE_SINGLE_END}
--APPLY_EAMSS_FILTER <Boolean>Apply EAMSS filtering to identify inappropriately quality scored bases towards the ends of
reads and convert their quality scores to Q2. Default value: true. Possible values:
{true, false}
--arguments_file <File> read one or more arguments files and add them to the command line This argument may be
specified 0 or more times. Default value: null.
--BARCODE_POPULATION_STRATEGY <PopulateBarcode>
When should the sample barcode (as read by the sequencer) be placed on the reads in the BC
tag? Default value: ORPHANS_ONLY. ORPHANS_ONLY (Put barcodes only into the records that
were not assigned to any declared barcode.)
INEXACT_MATCH (Put barcodes into records for which an exact match with a declared barcode
was not found.)
ALWAYS (Put barcodes into all the records.)
--BARCODES_DIR,-BCD <File> The barcodes directory with _barcode.txt files (generated by ExtractIlluminaBarcodes). If
not set, use BASECALLS_DIR. Default value: null.
--COMPRESS_OUTPUTS,-GZIP <Boolean>
Compress output FASTQ files using gzip and append a .gz extension to the file names.
Default value: false. Possible values: {true, false}
--COMPRESSION_LEVEL <Integer> Compression level for all compressed files created (e.g. BAM and VCF). Default value: 5.
--CREATE_INDEX <Boolean> Whether to create an index when writing VCF or coordinate sorted BAM output. Default
value: false. Possible values: {true, false}
--CREATE_MD5_FILE <Boolean> Whether to create an MD5 digest for any BAM or FASTQ files created. Default value:
false. Possible values: {true, false}
--DISTANCE_MODE <DistanceMetric>
The distance metric that should be used to compare the barcode-reads and the provided
barcodes for finding the best and second-best assignments. Default value: HAMMING.
HAMMING (Hamming distance: The n-th base in the read is compared against the n-th base in
the barcode. Unequal bases and low quality bases are considered mismatches. No-call
read-bases are not considered mismatches. )
LENIENT_HAMMING (Leniant Hamming distance: The n-th base in the read is compared against
the n-th base in the barcode. Unequal bases are considered mismatches. No-call read-bases,
or those with low quality are not considered mismatches.)
FREE (FREE Metric: A Levenshtein-like metric that performs a simple Smith-Waterman with
mismatch, gap open, and gap extend costs all equal to 1. Insertions or deletions at the
ends of the read or barcode do not count toward the distance. No-call read-bases, or those
with low quality are not considered mismatches.)
--FIRST_TILE <Integer> If set, this is the first tile to be processed (used for debugging). Note that tiles are
not processed in numerical order. Default value: null. Cannot be used in conjunction
with argument(s) PROCESS_SINGLE_TILE
--FIVE_PRIME_ADAPTER <String> For specifying adapters other than standard Illumina Default value: null.
--help,-h <Boolean> display the help message Default value: false. Possible values: {true, false}
--IGNORE_UNEXPECTED_BARCODES,-IGNORE_UNEXPECTED <Boolean>
Whether to ignore reads whose barcodes are not found in LIBRARY_PARAMS. Useful when
outputting SAM, BAM or CRAM files for only a subset of the barcodes in a lane. Default
value: false. Possible values: {true, false}
--INCLUDE_BARCODE_QUALITY <Boolean>
Should the barcode quality be included when the sample barcode is included? Default
value: false. Possible values: {true, false}
--INCLUDE_BC_IN_RG_TAG <Boolean>
Whether to include the barcode information in the @RG->BC header tag. Defaults to false
until included in the SAM spec. Default value: false. Possible values: {true, false}
--INCLUDE_NON_PF_READS,-NONPF <Boolean>
Whether to include non-PF reads Default value: true. Possible values: {true, false}
--INPUT_PARAMS_FILE <File> The input file that defines parameters for the program. This is the BARCODE_FILE for
`ExtractIlluminaBarcodes` or the MULTIPLEX_PARAMS or LIBRARY_PARAMS file for
`IlluminaBasecallsToFastq` or `IlluminaBasecallsToSam` Default value: null.
--LIBRARY_NAME,-LIB <String> Deprecated (use LIBRARY_PARAMS). The name of the sequenced library Default value: null.
Cannot be used in conjunction with argument(s) BARCODE_PARAMS LIBRARY_PARAMS
--MATCH_BARCODES_INLINE <Boolean>
If true, match barcodes on the fly. Otherwise parse the barcodes from the barcodes file.
Default value: false. Possible values: {true, false}
--MAX_MISMATCHES <Integer> Maximum mismatches for a barcode to be considered a match. Default value: 1.
--MAX_NO_CALLS <Integer> Maximum allowable number of no-calls in a barcode read before it is considered
unmatchable. Default value: 2.
--MAX_READS_IN_RAM_PER_TILE <Integer>
Configure SortingCollections to store this many records before spilling to disk. For an
indexed run, each SortingCollection gets this value/number of indices. Deprecated: use
`MAX_RECORDS_IN_RAM` Default value: -1.
--MAX_RECORDS_IN_RAM <Integer>When writing files that need to be sorted, this will specify the number of records stored
in RAM before spilling to disk. Increasing this number reduces the number of file handles
needed to sort the file, and increases the amount of RAM needed. Default value: 100.
--METRICS_FILE,-M <File> Per-barcode and per-lane metrics written to this file. Default value: null.
--MIN_MISMATCH_DELTA <Integer>Minimum difference between number of mismatches in the best and second best barcodes for a
barcode to be considered a match. Default value: 1.
--MINIMUM_BASE_QUALITY,-Q <Integer>
Minimum base quality. Any barcode bases falling below this quality will be considered a
mismatch even if the bases match. Default value: 0.
--MINIMUM_QUALITY <Integer> The minimum quality (after transforming 0s to 1s) expected from reads. If qualities are
lower than this value, an error is thrown. The default of 2 is what the Illumina's spec
describes as the minimum, but in practice the value has been observed lower. Default
value: 2.
--MOLECULAR_INDEX_BASE_QUALITY_TAG <String>
The tag to use to store any molecular index base qualities. If more than one molecular
index is found, their qualities will be concatenated and stored here (.i.e. the number of
"M" operators in the READ_STRUCTURE) Default value: QX.
--MOLECULAR_INDEX_TAG <String>The tag to use to store any molecular indexes. If more than one molecular index is found,
they will be concatenated and stored here. Default value: RX.
--NUM_PROCESSORS <Integer> The number of threads to run in parallel. If NUM_PROCESSORS = 0, number of cores is
automatically set to the number of cores available on the machine. If NUM_PROCESSORS < 0,
then the number of cores used will be the number available on the machine less
NUM_PROCESSORS. Default value: 0.
--PLATFORM <String> The name of the sequencing technology that produced the read. Default value: ILLUMINA.
--PROCESS_SINGLE_TILE <Integer>
If set, process only the tile number given and prepend the tile number to the output file
name. Default value: null. Cannot be used in conjunction with argument(s) FIRST_TILE
--QUIET <Boolean> Whether to suppress job-summary info on System.err. Default value: false. Possible
values: {true, false}
--READ_GROUP_ID,-RG <String> ID used to link RG header record with RG tag in SAM record. If these are unique in SAM
files that get merged, merge performance is better. If not specified, READ_GROUP_ID will
be set to <first 5 chars of RUN_BARCODE>.<LANE> . Default value: null.
--REFERENCE_SEQUENCE,-R <PicardHtsPath>
Reference sequence file. Default value: null.
--RUN_START_DATE <Date> The start date of the run. Default value: null.
--SORT <Boolean> If true, the output records are sorted by read name. Otherwise they are unsorted. Default
value: true. Possible values: {true, false}
--TAG_PER_MOLECULAR_INDEX <String>
The list of tags to store each molecular index. The number of tags should match the
number of molecular indexes. This argument may be specified 0 or more times. Default
value: null.
--THREE_PRIME_ADAPTER <String>For specifying adapters other than standard Illumina Default value: null.
--TILE_LIMIT <Integer> If set, process no more than this many tiles (used for debugging). Default value: null.
--TMP_DIR <File> One or more directories with space available to be used by this program for temporary
storage of working files This argument may be specified 0 or more times. Default value:
null.
--USE_JDK_DEFLATER,-use_jdk_deflater <Boolean>
Use the JDK Deflater instead of the Intel Deflater for writing compressed output Default
value: false. Possible values: {true, false}
--USE_JDK_INFLATER,-use_jdk_inflater <Boolean>
Use the JDK Inflater instead of the Intel Inflater for reading compressed input Default
value: false. Possible values: {true, false}
--VALIDATION_STRINGENCY <ValidationStringency>
Validation stringency for all SAM files read by this program. Setting stringency to
SILENT can improve performance when processing a BAM file in which variable-length data
(read, qualities, tags) do not otherwise need to be decoded. Default value: STRICT.
Possible values: {STRICT, LENIENT, SILENT}
--VERBOSITY <LogLevel> Control verbosity of logging. Default value: INFO. Possible values: {ERROR, WARNING,
INFO, DEBUG}
--version <Boolean> display the version number for this tool Default value: false. Possible values: {true,
false}
Advanced Arguments:
--showHidden <Boolean> display hidden arguments Default value: false. Possible values: {true, false}
The number of tags given in TAG_PER_MOLECULAR_INDEX does not match the number of molecular indexes in READ_STRUCTURE
USAGE: IlluminaBasecallsToSam [arguments]
Transforms raw Illumina sequencing data into an unmapped SAM, BAM or CRAM file.<p>The IlluminaBaseCallsToSam program
collects, demultiplexes, and sorts reads across all of the tiles of a lane via barcode to produce an unmapped SAM, BAM
or CRAM file. An unmapped BAM file is often referred to as a uBAM. All barcode, sample, and library data is provided
in the LIBRARY_PARAMS file. Note, this LIBRARY_PARAMS file should be formatted according to the specifications
indicated below. The following is an example of a properly formatted LIBRARY_PARAMS
file:</p>BARCODE_1 OUTPUT SAMPLE_ALIAS LIBRARY_NAME
AAAAAAAA SA_AAAAAAAA.bam SA_AAAAAAAA LN_AAAAAAAA
AAAAGAAG SA_AAAAGAAG.bam SA_AAAAGAAG LN_AAAAGAAG
AACAATGG SA_AACAATGG.bam SA_AACAATGG LN_AACAATGG
N SA_non_indexed.bam SA_non_indexed LN_NNNNNNNN
<p>The BARCODES_DIR file is produced by the <a
href='http://broadinstitute.github.io/picard/command-line-overview.html#ExtractIlluminaBarcodes'>ExtractIlluminaBarcodes</a>
tool for each lane of a flow cell.</p> <p>Barcode matching can be done inline without requiring barcodes files
generated by `ExtractIlluminaBarcode`. By setting MATCH_BARCODES_INLINE to true barcodes will be matched as they are
parsed and converted. Thisdoes not require BARCODES_DIR.</p> <h4>Usage example:</h4><pre>java -jar picard.jar
IlluminaBasecallsToSam \<br /> BASECALLS_DIR=/BaseCalls/ \<br /> LANE=001 \<br /> READ_STRUCTURE=25T8B25T
\<br /> RUN_BARCODE=run15 \<br /> IGNORE_UNEXPECTED_BARCODES=true \<br /> LIBRARY_PARAMS=library.params
</pre><hr />
Version:null
Required Arguments:
--BARCODE_PARAMS <File> Deprecated (use LIBRARY_PARAMS). Tab-separated file for creating all output SAM, BAM or
CRAM files for barcoded run with single IlluminaBasecallsToSam invocation. Columns are
BARCODE, OUTPUT, SAMPLE_ALIAS, and LIBRARY_NAME. Row with BARCODE=N is used to specify a
file for no barcode match Required. Cannot be used in conjunction with argument(s)
OUTPUT (O) SAMPLE_ALIAS (ALIAS) LIBRARY_NAME (LIB) LIBRARY_PARAMS
--BASECALLS_DIR,-B <File> The Illumina basecalls directory. Required.
--LANE,-L <Integer> Lane number. This can be specified multiple times. Reads with the same index in multiple
lanes will be added to the same output file. This argument must be specified at least
once. Required.
--LIBRARY_PARAMS <File> Tab-separated file for creating all output SAM, BAM or CRAM files for a lane with single
IlluminaBasecallsToSam invocation. The columns are OUTPUT, SAMPLE_ALIAS, and
LIBRARY_NAME, BARCODE_1, BARCODE_2 ... BARCODE_X where X = number of barcodes per cluster
(optional). Row with BARCODE_1 set to 'N' is used to specify a file for no barcode match.
You may also provide any 2 letter RG header attributes (excluding PU, CN, PL, and DT) as
columns in this file and the values for those columns will be inserted into the RG tag for
the SAM, BAM or CRAM file created for a given row. Required. Cannot be used in
conjunction with argument(s) OUTPUT (O) SAMPLE_ALIAS (ALIAS) LIBRARY_NAME (LIB)
BARCODE_PARAMS
--OUTPUT,-O <File> Deprecated (use LIBRARY_PARAMS). The output SAM, BAM or CRAM file. Format is determined
by extension. Required. Cannot be used in conjunction with argument(s) BARCODE_PARAMS
LIBRARY_PARAMS
--READ_STRUCTURE,-RS <String> A description of the logical structure of clusters in an Illumina Run, i.e. a description
of the structure IlluminaBasecallsToSam assumes the data to be in. It should consist of
integer/character pairs describing the number of cycles and the type of those cycles (B
for Sample Barcode, M for molecular barcode, T for Template, and S for skip). E.g. If the
input data consists of 80 base clusters and we provide a read structure of "28T8M8B8S28T"
then the sequence may be split up into four reads:
* read one with 28 cycles (bases) of template
* read two with 8 cycles (bases) of molecular barcode (ex. unique molecular barcode)
* read three with 8 cycles (bases) of sample barcode
* 8 cycles (bases) skipped.
* read four with 28 cycles (bases) of template
The skipped cycles would NOT be included in an output SAM/BAM file or in read groups
therein. Required.
--RUN_BARCODE <String> The barcode of the run. Prefixed to read names. Required.
--SAMPLE_ALIAS,-ALIAS <String>Deprecated (use LIBRARY_PARAMS). The name of the sequenced sample Required. Cannot be
used in conjunction with argument(s) BARCODE_PARAMS LIBRARY_PARAMS
--SEQUENCING_CENTER <String> The name of the sequencing center that produced the reads. Used to set the @RG->CN header
tag. Required.
Optional Arguments:
--ADAPTERS_TO_CHECK <IlluminaAdapterPair>
Which adapters to look for in the read. This argument may be specified 0 or more times.
Default value: [INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM]. Possible values:
{PAIRED_END, INDEXED, SINGLE_END, NEXTERA_V1, NEXTERA_V2, DUAL_INDEXED, FLUIDIGM,
TRUSEQ_SMALLRNA, ALTERNATIVE_SINGLE_END}
--APPLY_EAMSS_FILTER <Boolean>Apply EAMSS filtering to identify inappropriately quality scored bases towards the ends of
reads and convert their quality scores to Q2. Default value: true. Possible values:
{true, false}
--arguments_file <File> read one or more arguments files and add them to the command line This argument may be
specified 0 or more times. Default value: null.
--BARCODE_POPULATION_STRATEGY <PopulateBarcode>
When should the sample barcode (as read by the sequencer) be placed on the reads in the BC
tag? Default value: ORPHANS_ONLY. ORPHANS_ONLY (Put barcodes only into the records that
were not assigned to any declared barcode.)
INEXACT_MATCH (Put barcodes into records for which an exact match with a declared barcode
was not found.)
ALWAYS (Put barcodes into all the records.)
--BARCODES_DIR,-BCD <File> The barcodes directory with _barcode.txt files (generated by ExtractIlluminaBarcodes). If
not set, use BASECALLS_DIR. Default value: null.
--COMPRESS_OUTPUTS,-GZIP <Boolean>
Compress output FASTQ files using gzip and append a .gz extension to the file names.
Default value: false. Possible values: {true, false}
--COMPRESSION_LEVEL <Integer> Compression level for all compressed files created (e.g. BAM and VCF). Default value: 5.
--CREATE_INDEX <Boolean> Whether to create an index when writing VCF or coordinate sorted BAM output. Default
value: false. Possible values: {true, false}
--CREATE_MD5_FILE <Boolean> Whether to create an MD5 digest for any BAM or FASTQ files created. Default value:
false. Possible values: {true, false}
--DISTANCE_MODE <DistanceMetric>
The distance metric that should be used to compare the barcode-reads and the provided
barcodes for finding the best and second-best assignments. Default value: HAMMING.
HAMMING (Hamming distance: The n-th base in the read is compared against the n-th base in
the barcode. Unequal bases and low quality bases are considered mismatches. No-call
read-bases are not considered mismatches. )
LENIENT_HAMMING (Leniant Hamming distance: The n-th base in the read is compared against
the n-th base in the barcode. Unequal bases are considered mismatches. No-call read-bases,
or those with low quality are not considered mismatches.)
FREE (FREE Metric: A Levenshtein-like metric that performs a simple Smith-Waterman with
mismatch, gap open, and gap extend costs all equal to 1. Insertions or deletions at the
ends of the read or barcode do not count toward the distance. No-call read-bases, or those
with low quality are not considered mismatches.)
--FIRST_TILE <Integer> If set, this is the first tile to be processed (used for debugging). Note that tiles are
not processed in numerical order. Default value: null. Cannot be used in conjunction
with argument(s) PROCESS_SINGLE_TILE
--FIVE_PRIME_ADAPTER <String> For specifying adapters other than standard Illumina Default value: null.
--help,-h <Boolean> display the help message Default value: false. Possible values: {true, false}
--IGNORE_UNEXPECTED_BARCODES,-IGNORE_UNEXPECTED <Boolean>
Whether to ignore reads whose barcodes are not found in LIBRARY_PARAMS. Useful when
outputting SAM, BAM or CRAM files for only a subset of the barcodes in a lane. Default
value: false. Possible values: {true, false}
--INCLUDE_BARCODE_QUALITY <Boolean>
Should the barcode quality be included when the sample barcode is included? Default
value: false. Possible values: {true, false}
--INCLUDE_BC_IN_RG_TAG <Boolean>
Whether to include the barcode information in the @RG->BC header tag. Defaults to false
until included in the SAM spec. Default value: false. Possible values: {true, false}
--INCLUDE_NON_PF_READS,-NONPF <Boolean>
Whether to include non-PF reads Default value: true. Possible values: {true, false}
--INPUT_PARAMS_FILE <File> The input file that defines parameters for the program. This is the BARCODE_FILE for
`ExtractIlluminaBarcodes` or the MULTIPLEX_PARAMS or LIBRARY_PARAMS file for
`IlluminaBasecallsToFastq` or `IlluminaBasecallsToSam` Default value: null.
--LIBRARY_NAME,-LIB <String> Deprecated (use LIBRARY_PARAMS). The name of the sequenced library Default value: null.
Cannot be used in conjunction with argument(s) BARCODE_PARAMS LIBRARY_PARAMS
--MATCH_BARCODES_INLINE <Boolean>
If true, match barcodes on the fly. Otherwise parse the barcodes from the barcodes file.
Default value: false. Possible values: {true, false}
--MAX_MISMATCHES <Integer> Maximum mismatches for a barcode to be considered a match. Default value: 1.
--MAX_NO_CALLS <Integer> Maximum allowable number of no-calls in a barcode read before it is considered
unmatchable. Default value: 2.
--MAX_READS_IN_RAM_PER_TILE <Integer>
Configure SortingCollections to store this many records before spilling to disk. For an
indexed run, each SortingCollection gets this value/number of indices. Deprecated: use
`MAX_RECORDS_IN_RAM` Default value: -1.
--MAX_RECORDS_IN_RAM <Integer>When writing files that need to be sorted, this will specify the number of records stored
in RAM before spilling to disk. Increasing this number reduces the number of file handles
needed to sort the file, and increases the amount of RAM needed. Default value: 100.
--METRICS_FILE,-M <File> Per-barcode and per-lane metrics written to this file. Default value: null.
--MIN_MISMATCH_DELTA <Integer>Minimum difference between number of mismatches in the best and second best barcodes for a
barcode to be considered a match. Default value: 1.
--MINIMUM_BASE_QUALITY,-Q <Integer>
Minimum base quality. Any barcode bases falling below this quality will be considered a
mismatch even if the bases match. Default value: 0.
--MINIMUM_QUALITY <Integer> The minimum quality (after transforming 0s to 1s) expected from reads. If qualities are
lower than this value, an error is thrown. The default of 2 is what the Illumina's spec
describes as the minimum, but in practice the value has been observed lower. Default
value: 2.
--MOLECULAR_INDEX_BASE_QUALITY_TAG <String>
The tag to use to store any molecular index base qualities. If more than one molecular
index is found, their qualities will be concatenated and stored here (.i.e. the number of
"M" operators in the READ_STRUCTURE) Default value: QX.
--MOLECULAR_INDEX_TAG <String>The tag to use to store any molecular indexes. If more than one molecular index is found,
they will be concatenated and stored here. Default value: RX.
--NUM_PROCESSORS <Integer> The number of threads to run in parallel. If NUM_PROCESSORS = 0, number of cores is
automatically set to the number of cores available on the machine. If NUM_PROCESSORS < 0,
then the number of cores used will be the number available on the machine less
NUM_PROCESSORS. Default value: 0.
--PLATFORM <String> The name of the sequencing technology that produced the read. Default value: ILLUMINA.
--PROCESS_SINGLE_TILE <Integer>
If set, process only the tile number given and prepend the tile number to the output file
name. Default value: null. Cannot be used in conjunction with argument(s) FIRST_TILE
--QUIET <Boolean> Whether to suppress job-summary info on System.err. Default value: false. Possible
values: {true, false}
--READ_GROUP_ID,-RG <String> ID used to link RG header record with RG tag in SAM record. If these are unique in SAM
files that get merged, merge performance is better. If not specified, READ_GROUP_ID will
be set to <first 5 chars of RUN_BARCODE>.<LANE> . Default value: null.
--REFERENCE_SEQUENCE,-R <PicardHtsPath>
Reference sequence file. Default value: null.
--RUN_START_DATE <Date> The start date of the run. Default value: null.
--SORT <Boolean> If true, the output records are sorted by read name. Otherwise they are unsorted. Default
value: true. Possible values: {true, false}
--TAG_PER_MOLECULAR_INDEX <String>
The list of tags to store each molecular index. The number of tags should match the
number of molecular indexes. This argument may be specified 0 or more times. Default
value: null.
--THREE_PRIME_ADAPTER <String>For specifying adapters other than standard Illumina Default value: null.
--TILE_LIMIT <Integer> If set, process no more than this many tiles (used for debugging). Default value: null.
--TMP_DIR <File> One or more directories with space available to be used by this program for temporary
storage of working files This argument may be specified 0 or more times. Default value:
null.
--USE_JDK_DEFLATER,-use_jdk_deflater <Boolean>
Use the JDK Deflater instead of the Intel Deflater for writing compressed output Default
value: false. Possible values: {true, false}
--USE_JDK_INFLATER,-use_jdk_inflater <Boolean>
Use the JDK Inflater instead of the Intel Inflater for reading compressed input Default
value: false. Possible values: {true, false}
--VALIDATION_STRINGENCY <ValidationStringency>
Validation stringency for all SAM files read by this program. Setting stringency to
SILENT can improve performance when processing a BAM file in which variable-length data
(read, qualities, tags) do not otherwise need to be decoded. Default value: STRICT.
Possible values: {STRICT, LENIENT, SILENT}
--VERBOSITY <LogLevel> Control verbosity of logging. Default value: INFO. Possible values: {ERROR, WARNING,
INFO, DEBUG}
--version <Boolean> display the version number for this tool Default value: false. Possible values: {true,
false}
Advanced Arguments:
--showHidden <Boolean> display hidden arguments Default value: false. Possible values: {true, false}
The number of tags given in TAG_PER_MOLECULAR_INDEX does not match the number of molecular indexes in READ_STRUCTURE
USAGE: IlluminaBasecallsToSam [arguments]
Transforms raw Illumina sequencing data into an unmapped SAM, BAM or CRAM file.<p>The IlluminaBaseCallsToSam program
collects, demultiplexes, and sorts reads across all of the tiles of a lane via barcode to produce an unmapped SAM, BAM
or CRAM file. An unmapped BAM file is often referred to as a uBAM. All barcode, sample, and library data is provided
in the LIBRARY_PARAMS file. Note, this LIBRARY_PARAMS file should be formatted according to the specifications
indicated below. The following is an example of a properly formatted LIBRARY_PARAMS
file:</p>BARCODE_1 OUTPUT SAMPLE_ALIAS LIBRARY_NAME
AAAAAAAA SA_AAAAAAAA.bam SA_AAAAAAAA LN_AAAAAAAA
AAAAGAAG SA_AAAAGAAG.bam SA_AAAAGAAG LN_AAAAGAAG
AACAATGG SA_AACAATGG.bam SA_AACAATGG LN_AACAATGG
N SA_non_indexed.bam SA_non_indexed LN_NNNNNNNN
<p>The BARCODES_DIR file is produced by the <a
href='http://broadinstitute.github.io/picard/command-line-overview.html#ExtractIlluminaBarcodes'>ExtractIlluminaBarcodes</a>
tool for each lane of a flow cell.</p> <p>Barcode matching can be done inline without requiring barcodes files
generated by `ExtractIlluminaBarcode`. By setting MATCH_BARCODES_INLINE to true barcodes will be matched as they are
parsed and converted. Thisdoes not require BARCODES_DIR.</p> <h4>Usage example:</h4><pre>java -jar picard.jar
IlluminaBasecallsToSam \<br /> BASECALLS_DIR=/BaseCalls/ \<br /> LANE=001 \<br /> READ_STRUCTURE=25T8B25T
\<br /> RUN_BARCODE=run15 \<br /> IGNORE_UNEXPECTED_BARCODES=true \<br /> LIBRARY_PARAMS=library.params
</pre><hr />
Version:null
Required Arguments:
--BARCODE_PARAMS <File> Deprecated (use LIBRARY_PARAMS). Tab-separated file for creating all output SAM, BAM or
CRAM files for barcoded run with single IlluminaBasecallsToSam invocation. Columns are
BARCODE, OUTPUT, SAMPLE_ALIAS, and LIBRARY_NAME. Row with BARCODE=N is used to specify a
file for no barcode match Required. Cannot be used in conjunction with argument(s)
OUTPUT (O) SAMPLE_ALIAS (ALIAS) LIBRARY_NAME (LIB) LIBRARY_PARAMS
--BASECALLS_DIR,-B <File> The Illumina basecalls directory. Required.
--LANE,-L <Integer> Lane number. This can be specified multiple times. Reads with the same index in multiple
lanes will be added to the same output file. This argument must be specified at least
once. Required.
--LIBRARY_PARAMS <File> Tab-separated file for creating all output SAM, BAM or CRAM files for a lane with single
IlluminaBasecallsToSam invocation. The columns are OUTPUT, SAMPLE_ALIAS, and
LIBRARY_NAME, BARCODE_1, BARCODE_2 ... BARCODE_X where X = number of barcodes per cluster
(optional). Row with BARCODE_1 set to 'N' is used to specify a file for no barcode match.
You may also provide any 2 letter RG header attributes (excluding PU, CN, PL, and DT) as
columns in this file and the values for those columns will be inserted into the RG tag for
the SAM, BAM or CRAM file created for a given row. Required. Cannot be used in
conjunction with argument(s) OUTPUT (O) SAMPLE_ALIAS (ALIAS) LIBRARY_NAME (LIB)
BARCODE_PARAMS
--OUTPUT,-O <File> Deprecated (use LIBRARY_PARAMS). The output SAM, BAM or CRAM file. Format is determined
by extension. Required. Cannot be used in conjunction with argument(s) BARCODE_PARAMS
LIBRARY_PARAMS
--READ_STRUCTURE,-RS <String> A description of the logical structure of clusters in an Illumina Run, i.e. a description
of the structure IlluminaBasecallsToSam assumes the data to be in. It should consist of
integer/character pairs describing the number of cycles and the type of those cycles (B
for Sample Barcode, M for molecular barcode, T for Template, and S for skip). E.g. If the
input data consists of 80 base clusters and we provide a read structure of "28T8M8B8S28T"
then the sequence may be split up into four reads:
* read one with 28 cycles (bases) of template
* read two with 8 cycles (bases) of molecular barcode (ex. unique molecular barcode)
* read three with 8 cycles (bases) of sample barcode
* 8 cycles (bases) skipped.
* read four with 28 cycles (bases) of template
The skipped cycles would NOT be included in an output SAM/BAM file or in read groups
therein. Required.
--RUN_BARCODE <String> The barcode of the run. Prefixed to read names. Required.
--SAMPLE_ALIAS,-ALIAS <String>Deprecated (use LIBRARY_PARAMS). The name of the sequenced sample Required. Cannot be
used in conjunction with argument(s) BARCODE_PARAMS LIBRARY_PARAMS
--SEQUENCING_CENTER <String> The name of the sequencing center that produced the reads. Used to set the @RG->CN header
tag. Required.
Optional Arguments:
--ADAPTERS_TO_CHECK <IlluminaAdapterPair>
Which adapters to look for in the read. This argument may be specified 0 or more times.
Default value: [INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM]. Possible values:
{PAIRED_END, INDEXED, SINGLE_END, NEXTERA_V1, NEXTERA_V2, DUAL_INDEXED, FLUIDIGM,
TRUSEQ_SMALLRNA, ALTERNATIVE_SINGLE_END}
--APPLY_EAMSS_FILTER <Boolean>Apply EAMSS filtering to identify inappropriately quality scored bases towards the ends of
reads and convert their quality scores to Q2. Default value: true. Possible values:
{true, false}
--arguments_file <File> read one or more arguments files and add them to the command line This argument may be
specified 0 or more times. Default value: null.
--BARCODE_POPULATION_STRATEGY <PopulateBarcode>
When should the sample barcode (as read by the sequencer) be placed on the reads in the BC
tag? Default value: ORPHANS_ONLY. ORPHANS_ONLY (Put barcodes only into the records that
were not assigned to any declared barcode.)
INEXACT_MATCH (Put barcodes into records for which an exact match with a declared barcode
was not found.)
ALWAYS (Put barcodes into all the records.)
--BARCODES_DIR,-BCD <File> The barcodes directory with _barcode.txt files (generated by ExtractIlluminaBarcodes). If
not set, use BASECALLS_DIR. Default value: null.
--COMPRESS_OUTPUTS,-GZIP <Boolean>
Compress output FASTQ files using gzip and append a .gz extension to the file names.
Default value: false. Possible values: {true, false}
--COMPRESSION_LEVEL <Integer> Compression level for all compressed files created (e.g. BAM and VCF). Default value: 5.
--CREATE_INDEX <Boolean> Whether to create an index when writing VCF or coordinate sorted BAM output. Default
value: false. Possible values: {true, false}
--CREATE_MD5_FILE <Boolean> Whether to create an MD5 digest for any BAM or FASTQ files created. Default value:
false. Possible values: {true, false}
--DISTANCE_MODE <DistanceMetric>
The distance metric that should be used to compare the barcode-reads and the provided
barcodes for finding the best and second-best assignments. Default value: HAMMING.
HAMMING (Hamming distance: The n-th base in the read is compared against the n-th base in
the barcode. Unequal bases and low quality bases are considered mismatches. No-call
read-bases are not considered mismatches. )
LENIENT_HAMMING (Leniant Hamming distance: The n-th base in the read is compared against
the n-th base in the barcode. Unequal bases are considered mismatches. No-call read-bases,
or those with low quality are not considered mismatches.)
FREE (FREE Metric: A Levenshtein-like metric that performs a simple Smith-Waterman with
mismatch, gap open, and gap extend costs all equal to 1. Insertions or deletions at the
ends of the read or barcode do not count toward the distance. No-call read-bases, or those
with low quality are not considered mismatches.)
--FIRST_TILE <Integer> If set, this is the first tile to be processed (used for debugging). Note that tiles are
not processed in numerical order. Default value: null. Cannot be used in conjunction
with argument(s) PROCESS_SINGLE_TILE
--FIVE_PRIME_ADAPTER <String> For specifying adapters other than standard Illumina Default value: null.
--help,-h <Boolean> display the help message Default value: false. Possible values: {true, false}
--IGNORE_UNEXPECTED_BARCODES,-IGNORE_UNEXPECTED <Boolean>
Whether to ignore reads whose barcodes are not found in LIBRARY_PARAMS. Useful when
outputting SAM, BAM or CRAM files for only a subset of the barcodes in a lane. Default
value: false. Possible values: {true, false}
--INCLUDE_BARCODE_QUALITY <Boolean>
Should the barcode quality be included when the sample barcode is included? Default
value: false. Possible values: {true, false}
--INCLUDE_BC_IN_RG_TAG <Boolean>
Whether to include the barcode information in the @RG->BC header tag. Defaults to false
until included in the SAM spec. Default value: false. Possible values: {true, false}
--INCLUDE_NON_PF_READS,-NONPF <Boolean>
Whether to include non-PF reads Default value: true. Possible values: {true, false}
--INPUT_PARAMS_FILE <File> The input file that defines parameters for the program. This is the BARCODE_FILE for
`ExtractIlluminaBarcodes` or the MULTIPLEX_PARAMS or LIBRARY_PARAMS file for
`IlluminaBasecallsToFastq` or `IlluminaBasecallsToSam` Default value: null.
--LIBRARY_NAME,-LIB <String> Deprecated (use LIBRARY_PARAMS). The name of the sequenced library Default value: null.
Cannot be used in conjunction with argument(s) BARCODE_PARAMS LIBRARY_PARAMS
--MATCH_BARCODES_INLINE <Boolean>
If true, match barcodes on the fly. Otherwise parse the barcodes from the barcodes file.
Default value: false. Possible values: {true, false}
--MAX_MISMATCHES <Integer> Maximum mismatches for a barcode to be considered a match. Default value: 1.
--MAX_NO_CALLS <Integer> Maximum allowable number of no-calls in a barcode read before it is considered
unmatchable. Default value: 2.
--MAX_READS_IN_RAM_PER_TILE <Integer>
Configure SortingCollections to store this many records before spilling to disk. For an
indexed run, each SortingCollection gets this value/number of indices. Deprecated: use
`MAX_RECORDS_IN_RAM` Default value: -1.
--MAX_RECORDS_IN_RAM <Integer>When writing files that need to be sorted, this will specify the number of records stored
in RAM before spilling to disk. Increasing this number reduces the number of file handles
needed to sort the file, and increases the amount of RAM needed. Default value: 100.
--METRICS_FILE,-M <File> Per-barcode and per-lane metrics written to this file. Default value: null.
--MIN_MISMATCH_DELTA <Integer>Minimum difference between number of mismatches in the best and second best barcodes for a
barcode to be considered a match. Default value: 1.
--MINIMUM_BASE_QUALITY,-Q <Integer>
Minimum base quality. Any barcode bases falling below this quality will be considered a
mismatch even if the bases match. Default value: 0.
--MINIMUM_QUALITY <Integer> The minimum quality (after transforming 0s to 1s) expected from reads. If qualities are
lower than this value, an error is thrown. The default of 2 is what the Illumina's spec
describes as the minimum, but in practice the value has been observed lower. Default
value: 2.
--MOLECULAR_INDEX_BASE_QUALITY_TAG <String>
The tag to use to store any molecular index base qualities. If more than one molecular
index is found, their qualities will be concatenated and stored here (.i.e. the number of
"M" operators in the READ_STRUCTURE) Default value: QX.
--MOLECULAR_INDEX_TAG <String>The tag to use to store any molecular indexes. If more than one molecular index is found,
they will be concatenated and stored here. Default value: RX.
--NUM_PROCESSORS <Integer> The number of threads to run in parallel. If NUM_PROCESSORS = 0, number of cores is
automatically set to the number of cores available on the machine. If NUM_PROCESSORS < 0,
then the number of cores used will be the number available on the machine less
NUM_PROCESSORS. Default value: 0.
--PLATFORM <String> The name of the sequencing technology that produced the read. Default value: ILLUMINA.
--PROCESS_SINGLE_TILE <Integer>
If set, process only the tile number given and prepend the tile number to the output file
name. Default value: null. Cannot be used in conjunction with argument(s) FIRST_TILE
--QUIET <Boolean> Whether to suppress job-summary info on System.err. Default value: false. Possible
values: {true, false}
--READ_GROUP_ID,-RG <String> ID used to link RG header record with RG tag in SAM record. If these are unique in SAM
files that get merged, merge performance is better. If not specified, READ_GROUP_ID will
be set to <first 5 chars of RUN_BARCODE>.<LANE> . Default value: null.
--REFERENCE_SEQUENCE,-R <PicardHtsPath>
Reference sequence file. Default value: null.
--RUN_START_DATE <Date> The start date of the run. Default value: null.
--SORT <Boolean> If true, the output records are sorted by read name. Otherwise they are unsorted. Default
value: true. Possible values: {true, false}
--TAG_PER_MOLECULAR_INDEX <String>
The list of tags to store each molecular index. The number of tags should match the
number of molecular indexes. This argument may be specified 0 or more times. Default
value: null.
--THREE_PRIME_ADAPTER <String>For specifying adapters other than standard Illumina Default value: null.
--TILE_LIMIT <Integer> If set, process no more than this many tiles (used for debugging). Default value: null.
--TMP_DIR <File> One or more directories with space available to be used by this program for temporary
storage of working files This argument may be specified 0 or more times. Default value:
null.
--USE_JDK_DEFLATER,-use_jdk_deflater <Boolean>
Use the JDK Deflater instead of the Intel Deflater for writing compressed output Default
value: false. Possible values: {true, false}
--USE_JDK_INFLATER,-use_jdk_inflater <Boolean>
Use the JDK Inflater instead of the Intel Inflater for reading compressed input Default
value: false. Possible values: {true, false}
--VALIDATION_STRINGENCY <ValidationStringency>
Validation stringency for all SAM files read by this program. Setting stringency to
SILENT can improve performance when processing a BAM file in which variable-length data
(read, qualities, tags) do not otherwise need to be decoded. Default value: STRICT.
Possible values: {STRICT, LENIENT, SILENT}
--VERBOSITY <LogLevel> Control verbosity of logging. Default value: INFO. Possible values: {ERROR, WARNING,
INFO, DEBUG}
--version <Boolean> display the version number for this tool Default value: false. Possible values: {true,
false}
Advanced Arguments:
--showHidden <Boolean> display hidden arguments Default value: false. Possible values: {true, false}
The number of tags given in TAG_PER_MOLECULAR_INDEX does not match the number of molecular indexes in READ_STRUCTURE
USAGE: IlluminaBasecallsToSam [arguments]
Transforms raw Illumina sequencing data into an unmapped SAM, BAM or CRAM file.<p>The IlluminaBaseCallsToSam program
collects, demultiplexes, and sorts reads across all of the tiles of a lane via barcode to produce an unmapped SAM, BAM
or CRAM file. An unmapped BAM file is often referred to as a uBAM. All barcode, sample, and library data is provided
in the LIBRARY_PARAMS file. Note, this LIBRARY_PARAMS file should be formatted according to the specifications
indicated below. The following is an example of a properly formatted LIBRARY_PARAMS
file:</p>BARCODE_1 OUTPUT SAMPLE_ALIAS LIBRARY_NAME
AAAAAAAA SA_AAAAAAAA.bam SA_AAAAAAAA LN_AAAAAAAA
AAAAGAAG SA_AAAAGAAG.bam SA_AAAAGAAG LN_AAAAGAAG
AACAATGG SA_AACAATGG.bam SA_AACAATGG LN_AACAATGG
N SA_non_indexed.bam SA_non_indexed LN_NNNNNNNN
<p>The BARCODES_DIR file is produced by the <a
href='http://broadinstitute.github.io/picard/command-line-overview.html#ExtractIlluminaBarcodes'>ExtractIlluminaBarcodes</a>
tool for each lane of a flow cell.</p> <p>Barcode matching can be done inline without requiring barcodes files
generated by `ExtractIlluminaBarcode`. By setting MATCH_BARCODES_INLINE to true barcodes will be matched as they are
parsed and converted. Thisdoes not require BARCODES_DIR.</p> <h4>Usage example:</h4><pre>java -jar picard.jar
IlluminaBasecallsToSam \<br /> BASECALLS_DIR=/BaseCalls/ \<br /> LANE=001 \<br /> READ_STRUCTURE=25T8B25T
\<br /> RUN_BARCODE=run15 \<br /> IGNORE_UNEXPECTED_BARCODES=true \<br /> LIBRARY_PARAMS=library.params
</pre><hr />
Version:null
Required Arguments:
--BARCODE_PARAMS <File> Deprecated (use LIBRARY_PARAMS). Tab-separated file for creating all output SAM, BAM or
CRAM files for barcoded run with single IlluminaBasecallsToSam invocation. Columns are
BARCODE, OUTPUT, SAMPLE_ALIAS, and LIBRARY_NAME. Row with BARCODE=N is used to specify a
file for no barcode match Required. Cannot be used in conjunction with argument(s)
OUTPUT (O) SAMPLE_ALIAS (ALIAS) LIBRARY_NAME (LIB) LIBRARY_PARAMS
--BASECALLS_DIR,-B <File> The Illumina basecalls directory. Required.
--LANE,-L <Integer> Lane number. This can be specified multiple times. Reads with the same index in multiple
lanes will be added to the same output file. This argument must be specified at least
once. Required.
--LIBRARY_PARAMS <File> Tab-separated file for creating all output SAM, BAM or CRAM files for a lane with single
IlluminaBasecallsToSam invocation. The columns are OUTPUT, SAMPLE_ALIAS, and
LIBRARY_NAME, BARCODE_1, BARCODE_2 ... BARCODE_X where X = number of barcodes per cluster
(optional). Row with BARCODE_1 set to 'N' is used to specify a file for no barcode match.
You may also provide any 2 letter RG header attributes (excluding PU, CN, PL, and DT) as
columns in this file and the values for those columns will be inserted into the RG tag for
the SAM, BAM or CRAM file created for a given row. Required. Cannot be used in
conjunction with argument(s) OUTPUT (O) SAMPLE_ALIAS (ALIAS) LIBRARY_NAME (LIB)
BARCODE_PARAMS
--OUTPUT,-O <File> Deprecated (use LIBRARY_PARAMS). The output SAM, BAM or CRAM file. Format is determined
by extension. Required. Cannot be used in conjunction with argument(s) BARCODE_PARAMS
LIBRARY_PARAMS
--READ_STRUCTURE,-RS <String> A description of the logical structure of clusters in an Illumina Run, i.e. a description
of the structure IlluminaBasecallsToSam assumes the data to be in. It should consist of
integer/character pairs describing the number of cycles and the type of those cycles (B
for Sample Barcode, M for molecular barcode, T for Template, and S for skip). E.g. If the
input data consists of 80 base clusters and we provide a read structure of "28T8M8B8S28T"
then the sequence may be split up into four reads:
* read one with 28 cycles (bases) of template
* read two with 8 cycles (bases) of molecular barcode (ex. unique molecular barcode)
* read three with 8 cycles (bases) of sample barcode
* 8 cycles (bases) skipped.
* read four with 28 cycles (bases) of template
The skipped cycles would NOT be included in an output SAM/BAM file or in read groups
therein. Required.
--RUN_BARCODE <String> The barcode of the run. Prefixed to read names. Required.
--SAMPLE_ALIAS,-ALIAS <String>Deprecated (use LIBRARY_PARAMS). The name of the sequenced sample Required. Cannot be
used in conjunction with argument(s) BARCODE_PARAMS LIBRARY_PARAMS
--SEQUENCING_CENTER <String> The name of the sequencing center that produced the reads. Used to set the @RG->CN header
tag. Required.
Optional Arguments:
--ADAPTERS_TO_CHECK <IlluminaAdapterPair>
Which adapters to look for in the read. This argument may be specified 0 or more times.
Default value: [INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM]. Possible values:
{PAIRED_END, INDEXED, SINGLE_END, NEXTERA_V1, NEXTERA_V2, DUAL_INDEXED, FLUIDIGM,
TRUSEQ_SMALLRNA, ALTERNATIVE_SINGLE_END}
--APPLY_EAMSS_FILTER <Boolean>Apply EAMSS filtering to identify inappropriately quality scored bases towards the ends of
reads and convert their quality scores to Q2. Default value: true. Possible values:
{true, false}
--arguments_file <File> read one or more arguments files and add them to the command line This argument may be
specified 0 or more times. Default value: null.
--BARCODE_POPULATION_STRATEGY <PopulateBarcode>
When should the sample barcode (as read by the sequencer) be placed on the reads in the BC
tag? Default value: ORPHANS_ONLY. ORPHANS_ONLY (Put barcodes only into the records that
were not assigned to any declared barcode.)
INEXACT_MATCH (Put barcodes into records for which an exact match with a declared barcode
was not found.)
ALWAYS (Put barcodes into all the records.)
--BARCODES_DIR,-BCD <File> The barcodes directory with _barcode.txt files (generated by ExtractIlluminaBarcodes). If
not set, use BASECALLS_DIR. Default value: null.
--COMPRESS_OUTPUTS,-GZIP <Boolean>
Compress output FASTQ files using gzip and append a .gz extension to the file names.
Default value: false. Possible values: {true, false}
--COMPRESSION_LEVEL <Integer> Compression level for all compressed files created (e.g. BAM and VCF). Default value: 5.
--CREATE_INDEX <Boolean> Whether to create an index when writing VCF or coordinate sorted BAM output. Default
value: false. Possible values: {true, false}
--CREATE_MD5_FILE <Boolean> Whether to create an MD5 digest for any BAM or FASTQ files created. Default value:
false. Possible values: {true, false}
--DISTANCE_MODE <DistanceMetric>
The distance metric that should be used to compare the barcode-reads and the provided
barcodes for finding the best and second-best assignments. Default value: HAMMING.
HAMMING (Hamming distance: The n-th base in the read is compared against the n-th base in
the barcode. Unequal bases and low quality bases are considered mismatches. No-call
read-bases are not considered mismatches. )
LENIENT_HAMMING (Leniant Hamming distance: The n-th base in the read is compared against
the n-th base in the barcode. Unequal bases are considered mismatches. No-call read-bases,
or those with low quality are not considered mismatches.)
FREE (FREE Metric: A Levenshtein-like metric that performs a simple Smith-Waterman with
mismatch, gap open, and gap extend costs all equal to 1. Insertions or deletions at the
ends of the read or barcode do not count toward the distance. No-call read-bases, or those
with low quality are not considered mismatches.)
--FIRST_TILE <Integer> If set, this is the first tile to be processed (used for debugging). Note that tiles are
not processed in numerical order. Default value: null. Cannot be used in conjunction
with argument(s) PROCESS_SINGLE_TILE
--FIVE_PRIME_ADAPTER <String> For specifying adapters other than standard Illumina Default value: null.
--help,-h <Boolean> display the help message Default value: false. Possible values: {true, false}
--IGNORE_UNEXPECTED_BARCODES,-IGNORE_UNEXPECTED <Boolean>
Whether to ignore reads whose barcodes are not found in LIBRARY_PARAMS. Useful when
outputting SAM, BAM or CRAM files for only a subset of the barcodes in a lane. Default
value: false. Possible values: {true, false}
--INCLUDE_BARCODE_QUALITY <Boolean>
Should the barcode quality be included when the sample barcode is included? Default
value: false. Possible values: {true, false}
--INCLUDE_BC_IN_RG_TAG <Boolean>
Whether to include the barcode information in the @RG->BC header tag. Defaults to false
until included in the SAM spec. Default value: false. Possible values: {true, false}
--INCLUDE_NON_PF_READS,-NONPF <Boolean>
Whether to include non-PF reads Default value: true. Possible values: {true, false}
--INPUT_PARAMS_FILE <File> The input file that defines parameters for the program. This is the BARCODE_FILE for
`ExtractIlluminaBarcodes` or the MULTIPLEX_PARAMS or LIBRARY_PARAMS file for
`IlluminaBasecallsToFastq` or `IlluminaBasecallsToSam` Default value: null.
--LIBRARY_NAME,-LIB <String> Deprecated (use LIBRARY_PARAMS). The name of the sequenced library Default value: null.
Cannot be used in conjunction with argument(s) BARCODE_PARAMS LIBRARY_PARAMS
--MATCH_BARCODES_INLINE <Boolean>
If true, match barcodes on the fly. Otherwise parse the barcodes from the barcodes file.
Default value: false. Possible values: {true, false}
--MAX_MISMATCHES <Integer> Maximum mismatches for a barcode to be considered a match. Default value: 1.
--MAX_NO_CALLS <Integer> Maximum allowable number of no-calls in a barcode read before it is considered
unmatchable. Default value: 2.
--MAX_READS_IN_RAM_PER_TILE <Integer>
Configure SortingCollections to store this many records before spilling to disk. For an
indexed run, each SortingCollection gets this value/number of indices. Deprecated: use
`MAX_RECORDS_IN_RAM` Default value: -1.
--MAX_RECORDS_IN_RAM <Integer>When writing files that need to be sorted, this will specify the number of records stored
in RAM before spilling to disk. Increasing this number reduces the number of file handles
needed to sort the file, and increases the amount of RAM needed. Default value: 100.
--METRICS_FILE,-M <File> Per-barcode and per-lane metrics written to this file. Default value: null.
--MIN_MISMATCH_DELTA <Integer>Minimum difference between number of mismatches in the best and second best barcodes for a
barcode to be considered a match. Default value: 1.
--MINIMUM_BASE_QUALITY,-Q <Integer>
Minimum base quality. Any barcode bases falling below this quality will be considered a
mismatch even if the bases match. Default value: 0.
--MINIMUM_QUALITY <Integer> The minimum quality (after transforming 0s to 1s) expected from reads. If qualities are
lower than this value, an error is thrown. The default of 2 is what the Illumina's spec
describes as the minimum, but in practice the value has been observed lower. Default
value: 2.
--MOLECULAR_INDEX_BASE_QUALITY_TAG <String>
The tag to use to store any molecular index base qualities. If more than one molecular
index is found, their qualities will be concatenated and stored here (.i.e. the number of
"M" operators in the READ_STRUCTURE) Default value: QX.
--MOLECULAR_INDEX_TAG <String>The tag to use to store any molecular indexes. If more than one molecular index is found,
they will be concatenated and stored here. Default value: RX.
--NUM_PROCESSORS <Integer> The number of threads to run in parallel. If NUM_PROCESSORS = 0, number of cores is
automatically set to the number of cores available on the machine. If NUM_PROCESSORS < 0,
then the number of cores used will be the number available on the machine less
NUM_PROCESSORS. Default value: 0.
--PLATFORM <String> The name of the sequencing technology that produced the read. Default value: ILLUMINA.
--PROCESS_SINGLE_TILE <Integer>
If set, process only the tile number given and prepend the tile number to the output file
name. Default value: null. Cannot be used in conjunction with argument(s) FIRST_TILE
--QUIET <Boolean> Whether to suppress job-summary info on System.err. Default value: false. Possible
values: {true, false}
--READ_GROUP_ID,-RG <String> ID used to link RG header record with RG tag in SAM record. If these are unique in SAM
files that get merged, merge performance is better. If not specified, READ_GROUP_ID will
be set to <first 5 chars of RUN_BARCODE>.<LANE> . Default value: null.
--REFERENCE_SEQUENCE,-R <PicardHtsPath>
Reference sequence file. Default value: null.
--RUN_START_DATE <Date> The start date of the run. Default value: null.
--SORT <Boolean> If true, the output records are sorted by read name. Otherwise they are unsorted. Default
value: true. Possible values: {true, false}
--TAG_PER_MOLECULAR_INDEX <String>
The list of tags to store each molecular index. The number of tags should match the
number of molecular indexes. This argument may be specified 0 or more times. Default
value: null.
--THREE_PRIME_ADAPTER <String>For specifying adapters other than standard Illumina Default value: null.
--TILE_LIMIT <Integer> If set, process no more than this many tiles (used for debugging). Default value: null.
--TMP_DIR <File> One or more directories with space available to be used by this program for temporary
storage of working files This argument may be specified 0 or more times. Default value:
null.
--USE_JDK_DEFLATER,-use_jdk_deflater <Boolean>
Use the JDK Deflater instead of the Intel Deflater for writing compressed output Default
value: false. Possible values: {true, false}
--USE_JDK_INFLATER,-use_jdk_inflater <Boolean>
Use the JDK Inflater instead of the Intel Inflater for reading compressed input Default
value: false. Possible values: {true, false}
--VALIDATION_STRINGENCY <ValidationStringency>
Validation stringency for all SAM files read by this program. Setting stringency to
SILENT can improve performance when processing a BAM file in which variable-length data
(read, qualities, tags) do not otherwise need to be decoded. Default value: STRICT.
Possible values: {STRICT, LENIENT, SILENT}
--VERBOSITY <LogLevel> Control verbosity of logging. Default value: INFO. Possible values: {ERROR, WARNING,
INFO, DEBUG}
--version <Boolean> display the version number for this tool Default value: false. Possible values: {true,
false}
Advanced Arguments:
--showHidden <Boolean> display hidden arguments Default value: false. Possible values: {true, false}
The number of tags given in TAG_PER_MOLECULAR_INDEX does not match the number of molecular indexes in READ_STRUCTURE
USAGE: IlluminaBasecallsToSam [arguments]
Transforms raw Illumina sequencing data into an unmapped SAM, BAM or CRAM file.<p>The IlluminaBaseCallsToSam program
collects, demultiplexes, and sorts reads across all of the tiles of a lane via barcode to produce an unmapped SAM, BAM
or CRAM file. An unmapped BAM file is often referred to as a uBAM. All barcode, sample, and library data is provided
in the LIBRARY_PARAMS file. Note, this LIBRARY_PARAMS file should be formatted according to the specifications
indicated below. The following is an example of a properly formatted LIBRARY_PARAMS
file:</p>BARCODE_1 OUTPUT SAMPLE_ALIAS LIBRARY_NAME
AAAAAAAA SA_AAAAAAAA.bam SA_AAAAAAAA LN_AAAAAAAA
AAAAGAAG SA_AAAAGAAG.bam SA_AAAAGAAG LN_AAAAGAAG
AACAATGG SA_AACAATGG.bam SA_AACAATGG LN_AACAATGG
N SA_non_indexed.bam SA_non_indexed LN_NNNNNNNN
<p>The BARCODES_DIR file is produced by the <a
href='http://broadinstitute.github.io/picard/command-line-overview.html#ExtractIlluminaBarcodes'>ExtractIlluminaBarcodes</a>
tool for each lane of a flow cell.</p> <p>Barcode matching can be done inline without requiring barcodes files
generated by `ExtractIlluminaBarcode`. By setting MATCH_BARCODES_INLINE to true barcodes will be matched as they are
parsed and converted. Thisdoes not require BARCODES_DIR.</p> <h4>Usage example:</h4><pre>java -jar picard.jar
IlluminaBasecallsToSam \<br /> BASECALLS_DIR=/BaseCalls/ \<br /> LANE=001 \<br /> READ_STRUCTURE=25T8B25T
\<br /> RUN_BARCODE=run15 \<br /> IGNORE_UNEXPECTED_BARCODES=true \<br /> LIBRARY_PARAMS=library.params
</pre><hr />
Version:null
Required Arguments:
--BARCODE_PARAMS <File> Deprecated (use LIBRARY_PARAMS). Tab-separated file for creating all output SAM, BAM or
CRAM files for barcoded run with single IlluminaBasecallsToSam invocation. Columns are
BARCODE, OUTPUT, SAMPLE_ALIAS, and LIBRARY_NAME. Row with BARCODE=N is used to specify a
file for no barcode match Required. Cannot be used in conjunction with argument(s)
OUTPUT (O) SAMPLE_ALIAS (ALIAS) LIBRARY_NAME (LIB) LIBRARY_PARAMS
--BASECALLS_DIR,-B <File> The Illumina basecalls directory. Required.
--LANE,-L <Integer> Lane number. This can be specified multiple times. Reads with the same index in multiple
lanes will be added to the same output file. This argument must be specified at least
once. Required.
--LIBRARY_PARAMS <File> Tab-separated file for creating all output SAM, BAM or CRAM files for a lane with single
IlluminaBasecallsToSam invocation. The columns are OUTPUT, SAMPLE_ALIAS, and
LIBRARY_NAME, BARCODE_1, BARCODE_2 ... BARCODE_X where X = number of barcodes per cluster
(optional). Row with BARCODE_1 set to 'N' is used to specify a file for no barcode match.
You may also provide any 2 letter RG header attributes (excluding PU, CN, PL, and DT) as
columns in this file and the values for those columns will be inserted into the RG tag for
the SAM, BAM or CRAM file created for a given row. Required. Cannot be used in
conjunction with argument(s) OUTPUT (O) SAMPLE_ALIAS (ALIAS) LIBRARY_NAME (LIB)
BARCODE_PARAMS
--OUTPUT,-O <File> Deprecated (use LIBRARY_PARAMS). The output SAM, BAM or CRAM file. Format is determined
by extension. Required. Cannot be used in conjunction with argument(s) BARCODE_PARAMS
LIBRARY_PARAMS
--READ_STRUCTURE,-RS <String> A description of the logical structure of clusters in an Illumina Run, i.e. a description
of the structure IlluminaBasecallsToSam assumes the data to be in. It should consist of
integer/character pairs describing the number of cycles and the type of those cycles (B
for Sample Barcode, M for molecular barcode, T for Template, and S for skip). E.g. If the
input data consists of 80 base clusters and we provide a read structure of "28T8M8B8S28T"
then the sequence may be split up into four reads:
* read one with 28 cycles (bases) of template
* read two with 8 cycles (bases) of molecular barcode (ex. unique molecular barcode)
* read three with 8 cycles (bases) of sample barcode
* 8 cycles (bases) skipped.
* read four with 28 cycles (bases) of template
The skipped cycles would NOT be included in an output SAM/BAM file or in read groups
therein. Required.
--RUN_BARCODE <String> The barcode of the run. Prefixed to read names. Required.
--SAMPLE_ALIAS,-ALIAS <String>Deprecated (use LIBRARY_PARAMS). The name of the sequenced sample Required. Cannot be
used in conjunction with argument(s) BARCODE_PARAMS LIBRARY_PARAMS
--SEQUENCING_CENTER <String> The name of the sequencing center that produced the reads. Used to set the @RG->CN header
tag. Required.
Optional Arguments:
--ADAPTERS_TO_CHECK <IlluminaAdapterPair>
Which adapters to look for in the read. This argument may be specified 0 or more times.
Default value: [INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM]. Possible values:
{PAIRED_END, INDEXED, SINGLE_END, NEXTERA_V1, NEXTERA_V2, DUAL_INDEXED, FLUIDIGM,
TRUSEQ_SMALLRNA, ALTERNATIVE_SINGLE_END}
--APPLY_EAMSS_FILTER <Boolean>Apply EAMSS filtering to identify inappropriately quality scored bases towards the ends of
reads and convert their quality scores to Q2. Default value: true. Possible values:
{true, false}
--arguments_file <File> read one or more arguments files and add them to the command line This argument may be
specified 0 or more times. Default value: null.
--BARCODE_POPULATION_STRATEGY <PopulateBarcode>
When should the sample barcode (as read by the sequencer) be placed on the reads in the BC
tag? Default value: ORPHANS_ONLY. ORPHANS_ONLY (Put barcodes only into the records that
were not assigned to any declared barcode.)
INEXACT_MATCH (Put barcodes into records for which an exact match with a declared barcode
was not found.)
ALWAYS (Put barcodes into all the records.)
--BARCODES_DIR,-BCD <File> The barcodes directory with _barcode.txt files (generated by ExtractIlluminaBarcodes). If
not set, use BASECALLS_DIR. Default value: null.
--COMPRESS_OUTPUTS,-GZIP <Boolean>
Compress output FASTQ files using gzip and append a .gz extension to the file names.
Default value: false. Possible values: {true, false}
--COMPRESSION_LEVEL <Integer> Compression level for all compressed files created (e.g. BAM and VCF). Default value: 5.
--CREATE_INDEX <Boolean> Whether to create an index when writing VCF or coordinate sorted BAM output. Default
value: false. Possible values: {true, false}
--CREATE_MD5_FILE <Boolean> Whether to create an MD5 digest for any BAM or FASTQ files created. Default value:
false. Possible values: {true, false}
--DISTANCE_MODE <DistanceMetric>
The distance metric that should be used to compare the barcode-reads and the provided
barcodes for finding the best and second-best assignments. Default value: HAMMING.
HAMMING (Hamming distance: The n-th base in the read is compared against the n-th base in
the barcode. Unequal bases and low quality bases are considered mismatches. No-call
read-bases are not considered mismatches. )
LENIENT_HAMMING (Leniant Hamming distance: The n-th base in the read is compared against
the n-th base in the barcode. Unequal bases are considered mismatches. No-call read-bases,
or those with low quality are not considered mismatches.)
FREE (FREE Metric: A Levenshtein-like metric that performs a simple Smith-Waterman with
mismatch, gap open, and gap extend costs all equal to 1. Insertions or deletions at the
ends of the read or barcode do not count toward the distance. No-call read-bases, or those
with low quality are not considered mismatches.)
--FIRST_TILE <Integer> If set, this is the first tile to be processed (used for debugging). Note that tiles are
not processed in numerical order. Default value: null. Cannot be used in conjunction
with argument(s) PROCESS_SINGLE_TILE
--FIVE_PRIME_ADAPTER <String> For specifying adapters other than standard Illumina Default value: null.
--help,-h <Boolean> display the help message Default value: false. Possible values: {true, false}
--IGNORE_UNEXPECTED_BARCODES,-IGNORE_UNEXPECTED <Boolean>
Whether to ignore reads whose barcodes are not found in LIBRARY_PARAMS. Useful when
outputting SAM, BAM or CRAM files for only a subset of the barcodes in a lane. Default
value: false. Possible values: {true, false}
--INCLUDE_BARCODE_QUALITY <Boolean>
Should the barcode quality be included when the sample barcode is included? Default
value: false. Possible values: {true, false}
--INCLUDE_BC_IN_RG_TAG <Boolean>
Whether to include the barcode information in the @RG->BC header tag. Defaults to false
until included in the SAM spec. Default value: false. Possible values: {true, false}
--INCLUDE_NON_PF_READS,-NONPF <Boolean>
Whether to include non-PF reads Default value: true. Possible values: {true, false}
--INPUT_PARAMS_FILE <File> The input file that defines parameters for the program. This is the BARCODE_FILE for
`ExtractIlluminaBarcodes` or the MULTIPLEX_PARAMS or LIBRARY_PARAMS file for
`IlluminaBasecallsToFastq` or `IlluminaBasecallsToSam` Default value: null.
--LIBRARY_NAME,-LIB <String> Deprecated (use LIBRARY_PARAMS). The name of the sequenced library Default value: null.
Cannot be used in conjunction with argument(s) BARCODE_PARAMS LIBRARY_PARAMS
--MATCH_BARCODES_INLINE <Boolean>
If true, match barcodes on the fly. Otherwise parse the barcodes from the barcodes file.
Default value: false. Possible values: {true, false}
--MAX_MISMATCHES <Integer> Maximum mismatches for a barcode to be considered a match. Default value: 1.
--MAX_NO_CALLS <Integer> Maximum allowable number of no-calls in a barcode read before it is considered
unmatchable. Default value: 2.
--MAX_READS_IN_RAM_PER_TILE <Integer>
Configure SortingCollections to store this many records before spilling to disk. For an
indexed run, each SortingCollection gets this value/number of indices. Deprecated: use
`MAX_RECORDS_IN_RAM` Default value: -1.
--MAX_RECORDS_IN_RAM <Integer>When writing files that need to be sorted, this will specify the number of records stored
in RAM before spilling to disk. Increasing this number reduces the number of file handles
needed to sort the file, and increases the amount of RAM needed. Default value: 100.
--METRICS_FILE,-M <File> Per-barcode and per-lane metrics written to this file. Default value: null.
--MIN_MISMATCH_DELTA <Integer>Minimum difference between number of mismatches in the best and second best barcodes for a
barcode to be considered a match. Default value: 1.
--MINIMUM_BASE_QUALITY,-Q <Integer>
Minimum base quality. Any barcode bases falling below this quality will be considered a
mismatch even if the bases match. Default value: 0.
--MINIMUM_QUALITY <Integer> The minimum quality (after transforming 0s to 1s) expected from reads. If qualities are
lower than this value, an error is thrown. The default of 2 is what the Illumina's spec
describes as the minimum, but in practice the value has been observed lower. Default
value: 2.
--MOLECULAR_INDEX_BASE_QUALITY_TAG <String>
The tag to use to store any molecular index base qualities. If more than one molecular
index is found, their qualities will be concatenated and stored here (.i.e. the number of
"M" operators in the READ_STRUCTURE) Default value: QX.
--MOLECULAR_INDEX_TAG <String>The tag to use to store any molecular indexes. If more than one molecular index is found,
they will be concatenated and stored here. Default value: RX.
--NUM_PROCESSORS <Integer> The number of threads to run in parallel. If NUM_PROCESSORS = 0, number of cores is
automatically set to the number of cores available on the machine. If NUM_PROCESSORS < 0,
then the number of cores used will be the number available on the machine less
NUM_PROCESSORS. Default value: 0.
--PLATFORM <String> The name of the sequencing technology that produced the read. Default value: ILLUMINA.
--PROCESS_SINGLE_TILE <Integer>
If set, process only the tile number given and prepend the tile number to the output file
name. Default value: null. Cannot be used in conjunction with argument(s) FIRST_TILE
--QUIET <Boolean> Whether to suppress job-summary info on System.err. Default value: false. Possible
values: {true, false}
--READ_GROUP_ID,-RG <String> ID used to link RG header record with RG tag in SAM record. If these are unique in SAM
files that get merged, merge performance is better. If not specified, READ_GROUP_ID will
be set to <first 5 chars of RUN_BARCODE>.<LANE> . Default value: null.
--REFERENCE_SEQUENCE,-R <PicardHtsPath>
Reference sequence file. Default value: null.
--RUN_START_DATE <Date> The start date of the run. Default value: null.
--SORT <Boolean> If true, the output records are sorted by read name. Otherwise they are unsorted. Default
value: true. Possible values: {true, false}
--TAG_PER_MOLECULAR_INDEX <String>
The list of tags to store each molecular index. The number of tags should match the
number of molecular indexes. This argument may be specified 0 or more times. Default
value: null.
--THREE_PRIME_ADAPTER <String>For specifying adapters other than standard Illumina Default value: null.
--TILE_LIMIT <Integer> If set, process no more than this many tiles (used for debugging). Default value: null.
--TMP_DIR <File> One or more directories with space available to be used by this program for temporary
storage of working files This argument may be specified 0 or more times. Default value:
null.
--USE_JDK_DEFLATER,-use_jdk_deflater <Boolean>
Use the JDK Deflater instead of the Intel Deflater for writing compressed output Default
value: false. Possible values: {true, false}
--USE_JDK_INFLATER,-use_jdk_inflater <Boolean>
Use the JDK Inflater instead of the Intel Inflater for reading compressed input Default
value: false. Possible values: {true, false}
--VALIDATION_STRINGENCY <ValidationStringency>
Validation stringency for all SAM files read by this program. Setting stringency to
SILENT can improve performance when processing a BAM file in which variable-length data
(read, qualities, tags) do not otherwise need to be decoded. Default value: STRICT.
Possible values: {STRICT, LENIENT, SILENT}
--VERBOSITY <LogLevel> Control verbosity of logging. Default value: INFO. Possible values: {ERROR, WARNING,
INFO, DEBUG}
--version <Boolean> display the version number for this tool Default value: false. Possible values: {true,
false}
Advanced Arguments:
--showHidden <Boolean> display hidden arguments Default value: false. Possible values: {true, false}
The number of tags given in TAG_PER_MOLECULAR_INDEX does not match the number of molecular indexes in READ_STRUCTURE
USAGE: IlluminaBasecallsToSam [arguments]
Transforms raw Illumina sequencing data into an unmapped SAM, BAM or CRAM file.<p>The IlluminaBaseCallsToSam program
collects, demultiplexes, and sorts reads across all of the tiles of a lane via barcode to produce an unmapped SAM, BAM
or CRAM file. An unmapped BAM file is often referred to as a uBAM. All barcode, sample, and library data is provided
in the LIBRARY_PARAMS file. Note, this LIBRARY_PARAMS file should be formatted according to the specifications
indicated below. The following is an example of a properly formatted LIBRARY_PARAMS
file:</p>BARCODE_1 OUTPUT SAMPLE_ALIAS LIBRARY_NAME
AAAAAAAA SA_AAAAAAAA.bam SA_AAAAAAAA LN_AAAAAAAA
AAAAGAAG SA_AAAAGAAG.bam SA_AAAAGAAG LN_AAAAGAAG
AACAATGG SA_AACAATGG.bam SA_AACAATGG LN_AACAATGG
N SA_non_indexed.bam SA_non_indexed LN_NNNNNNNN
<p>The BARCODES_DIR file is produced by the <a
href='http://broadinstitute.github.io/picard/command-line-overview.html#ExtractIlluminaBarcodes'>ExtractIlluminaBarcodes</a>
tool for each lane of a flow cell.</p> <p>Barcode matching can be done inline without requiring barcodes files
generated by `ExtractIlluminaBarcode`. By setting MATCH_BARCODES_INLINE to true barcodes will be matched as they are
parsed and converted. Thisdoes not require BARCODES_DIR.</p> <h4>Usage example:</h4><pre>java -jar picard.jar
IlluminaBasecallsToSam \<br /> BASECALLS_DIR=/BaseCalls/ \<br /> LANE=001 \<br /> READ_STRUCTURE=25T8B25T
\<br /> RUN_BARCODE=run15 \<br /> IGNORE_UNEXPECTED_BARCODES=true \<br /> LIBRARY_PARAMS=library.params
</pre><hr />
Version:null
Required Arguments:
--BARCODE_PARAMS <File> Deprecated (use LIBRARY_PARAMS). Tab-separated file for creating all output SAM, BAM or
CRAM files for barcoded run with single IlluminaBasecallsToSam invocation. Columns are
BARCODE, OUTPUT, SAMPLE_ALIAS, and LIBRARY_NAME. Row with BARCODE=N is used to specify a
file for no barcode match Required. Cannot be used in conjunction with argument(s)
OUTPUT (O) SAMPLE_ALIAS (ALIAS) LIBRARY_NAME (LIB) LIBRARY_PARAMS
--BASECALLS_DIR,-B <File> The Illumina basecalls directory. Required.
--LANE,-L <Integer> Lane number. This can be specified multiple times. Reads with the same index in multiple
lanes will be added to the same output file. This argument must be specified at least
once. Required.
--LIBRARY_PARAMS <File> Tab-separated file for creating all output SAM, BAM or CRAM files for a lane with single
IlluminaBasecallsToSam invocation. The columns are OUTPUT, SAMPLE_ALIAS, and
LIBRARY_NAME, BARCODE_1, BARCODE_2 ... BARCODE_X where X = number of barcodes per cluster
(optional). Row with BARCODE_1 set to 'N' is used to specify a file for no barcode match.
You may also provide any 2 letter RG header attributes (excluding PU, CN, PL, and DT) as
columns in this file and the values for those columns will be inserted into the RG tag for
the SAM, BAM or CRAM file created for a given row. Required. Cannot be used in
conjunction with argument(s) OUTPUT (O) SAMPLE_ALIAS (ALIAS) LIBRARY_NAME (LIB)
BARCODE_PARAMS
--OUTPUT,-O <File> Deprecated (use LIBRARY_PARAMS). The output SAM, BAM or CRAM file. Format is determined
by extension. Required. Cannot be used in conjunction with argument(s) BARCODE_PARAMS
LIBRARY_PARAMS
--READ_STRUCTURE,-RS <String> A description of the logical structure of clusters in an Illumina Run, i.e. a description
of the structure IlluminaBasecallsToSam assumes the data to be in. It should consist of
integer/character pairs describing the number of cycles and the type of those cycles (B
for Sample Barcode, M for molecular barcode, T for Template, and S for skip). E.g. If the
input data consists of 80 base clusters and we provide a read structure of "28T8M8B8S28T"
then the sequence may be split up into four reads:
* read one with 28 cycles (bases) of template
* read two with 8 cycles (bases) of molecular barcode (ex. unique molecular barcode)
* read three with 8 cycles (bases) of sample barcode
* 8 cycles (bases) skipped.
* read four with 28 cycles (bases) of template
The skipped cycles would NOT be included in an output SAM/BAM file or in read groups
therein. Required.
--RUN_BARCODE <String> The barcode of the run. Prefixed to read names. Required.
--SAMPLE_ALIAS,-ALIAS <String>Deprecated (use LIBRARY_PARAMS). The name of the sequenced sample Required. Cannot be
used in conjunction with argument(s) BARCODE_PARAMS LIBRARY_PARAMS
--SEQUENCING_CENTER <String> The name of the sequencing center that produced the reads. Used to set the @RG->CN header
tag. Required.
Optional Arguments:
--ADAPTERS_TO_CHECK <IlluminaAdapterPair>
Which adapters to look for in the read. This argument may be specified 0 or more times.
Default value: [INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM]. Possible values:
{PAIRED_END, INDEXED, SINGLE_END, NEXTERA_V1, NEXTERA_V2, DUAL_INDEXED, FLUIDIGM,
TRUSEQ_SMALLRNA, ALTERNATIVE_SINGLE_END}
--APPLY_EAMSS_FILTER <Boolean>Apply EAMSS filtering to identify inappropriately quality scored bases towards the ends of
reads and convert their quality scores to Q2. Default value: true. Possible values:
{true, false}
--arguments_file <File> read one or more arguments files and add them to the command line This argument may be
specified 0 or more times. Default value: null.
--BARCODE_POPULATION_STRATEGY <PopulateBarcode>
When should the sample barcode (as read by the sequencer) be placed on the reads in the BC
tag? Default value: ORPHANS_ONLY. ORPHANS_ONLY (Put barcodes only into the records that
were not assigned to any declared barcode.)
INEXACT_MATCH (Put barcodes into records for which an exact match with a declared barcode
was not found.)
ALWAYS (Put barcodes into all the records.)
--BARCODES_DIR,-BCD <File> The barcodes directory with _barcode.txt files (generated by ExtractIlluminaBarcodes). If
not set, use BASECALLS_DIR. Default value: null.
--COMPRESS_OUTPUTS,-GZIP <Boolean>
Compress output FASTQ files using gzip and append a .gz extension to the file names.
Default value: false. Possible values: {true, false}
--COMPRESSION_LEVEL <Integer> Compression level for all compressed files created (e.g. BAM and VCF). Default value: 5.
--CREATE_INDEX <Boolean> Whether to create an index when writing VCF or coordinate sorted BAM output. Default
value: false. Possible values: {true, false}
--CREATE_MD5_FILE <Boolean> Whether to create an MD5 digest for any BAM or FASTQ files created. Default value:
false. Possible values: {true, false}
--DISTANCE_MODE <DistanceMetric>
The distance metric that should be used to compare the barcode-reads and the provided
barcodes for finding the best and second-best assignments. Default value: HAMMING.
HAMMING (Hamming distance: The n-th base in the read is compared against the n-th base in
the barcode. Unequal bases and low quality bases are considered mismatches. No-call
read-bases are not considered mismatches. )
LENIENT_HAMMING (Leniant Hamming distance: The n-th base in the read is compared against
the n-th base in the barcode. Unequal bases are considered mismatches. No-call read-bases,
or those with low quality are not considered mismatches.)
FREE (FREE Metric: A Levenshtein-like metric that performs a simple Smith-Waterman with
mismatch, gap open, and gap extend costs all equal to 1. Insertions or deletions at the
ends of the read or barcode do not count toward the distance. No-call read-bases, or those
with low quality are not considered mismatches.)
--FIRST_TILE <Integer> If set, this is the first tile to be processed (used for debugging). Note that tiles are
not processed in numerical order. Default value: null. Cannot be used in conjunction
with argument(s) PROCESS_SINGLE_TILE
--FIVE_PRIME_ADAPTER <String> For specifying adapters other than standard Illumina Default value: null.
--help,-h <Boolean> display the help message Default value: false. Possible values: {true, false}
--IGNORE_UNEXPECTED_BARCODES,-IGNORE_UNEXPECTED <Boolean>
Whether to ignore reads whose barcodes are not found in LIBRARY_PARAMS. Useful when
outputting SAM, BAM or CRAM files for only a subset of the barcodes in a lane. Default
value: false. Possible values: {true, false}
--INCLUDE_BARCODE_QUALITY <Boolean>
Should the barcode quality be included when the sample barcode is included? Default
value: false. Possible values: {true, false}
--INCLUDE_BC_IN_RG_TAG <Boolean>
Whether to include the barcode information in the @RG->BC header tag. Defaults to false
until included in the SAM spec. Default value: false. Possible values: {true, false}
--INCLUDE_NON_PF_READS,-NONPF <Boolean>
Whether to include non-PF reads Default value: true. Possible values: {true, false}
--INPUT_PARAMS_FILE <File> The input file that defines parameters for the program. This is the BARCODE_FILE for
`ExtractIlluminaBarcodes` or the MULTIPLEX_PARAMS or LIBRARY_PARAMS file for
`IlluminaBasecallsToFastq` or `IlluminaBasecallsToSam` Default value: null.
--LIBRARY_NAME,-LIB <String> Deprecated (use LIBRARY_PARAMS). The name of the sequenced library Default value: null.
Cannot be used in conjunction with argument(s) BARCODE_PARAMS LIBRARY_PARAMS
--MATCH_BARCODES_INLINE <Boolean>
If true, match barcodes on the fly. Otherwise parse the barcodes from the barcodes file.
Default value: false. Possible values: {true, false}
--MAX_MISMATCHES <Integer> Maximum mismatches for a barcode to be considered a match. Default value: 1.
--MAX_NO_CALLS <Integer> Maximum allowable number of no-calls in a barcode read before it is considered
unmatchable. Default value: 2.
--MAX_READS_IN_RAM_PER_TILE <Integer>
Configure SortingCollections to store this many records before spilling to disk. For an
indexed run, each SortingCollection gets this value/number of indices. Deprecated: use
`MAX_RECORDS_IN_RAM` Default value: -1.
--MAX_RECORDS_IN_RAM <Integer>When writing files that need to be sorted, this will specify the number of records stored
in RAM before spilling to disk. Increasing this number reduces the number of file handles
needed to sort the file, and increases the amount of RAM needed. Default value: 100.
--METRICS_FILE,-M <File> Per-barcode and per-lane metrics written to this file. Default value: null.
--MIN_MISMATCH_DELTA <Integer>Minimum difference between number of mismatches in the best and second best barcodes for a
barcode to be considered a match. Default value: 1.
--MINIMUM_BASE_QUALITY,-Q <Integer>
Minimum base quality. Any barcode bases falling below this quality will be considered a
mismatch even if the bases match. Default value: 0.
--MINIMUM_QUALITY <Integer> The minimum quality (after transforming 0s to 1s) expected from reads. If qualities are
lower than this value, an error is thrown. The default of 2 is what the Illumina's spec
describes as the minimum, but in practice the value has been observed lower. Default
value: 2.
--MOLECULAR_INDEX_BASE_QUALITY_TAG <String>
The tag to use to store any molecular index base qualities. If more than one molecular
index is found, their qualities will be concatenated and stored here (.i.e. the number of
"M" operators in the READ_STRUCTURE) Default value: QX.
--MOLECULAR_INDEX_TAG <String>The tag to use to store any molecular indexes. If more than one molecular index is found,
they will be concatenated and stored here. Default value: RX.
--NUM_PROCESSORS <Integer> The number of threads to run in parallel. If NUM_PROCESSORS = 0, number of cores is
automatically set to the number of cores available on the machine. If NUM_PROCESSORS < 0,
then the number of cores used will be the number available on the machine less
NUM_PROCESSORS. Default value: 0.
--PLATFORM <String> The name of the sequencing technology that produced the read. Default value: ILLUMINA.
--PROCESS_SINGLE_TILE <Integer>
If set, process only the tile number given and prepend the tile number to the output file
name. Default value: null. Cannot be used in conjunction with argument(s) FIRST_TILE
--QUIET <Boolean> Whether to suppress job-summary info on System.err. Default value: false. Possible
values: {true, false}
--READ_GROUP_ID,-RG <String> ID used to link RG header record with RG tag in SAM record. If these are unique in SAM
files that get merged, merge performance is better. If not specified, READ_GROUP_ID will
be set to <first 5 chars of RUN_BARCODE>.<LANE> . Default value: null.
--REFERENCE_SEQUENCE,-R <PicardHtsPath>
Reference sequence file. Default value: null.
--RUN_START_DATE <Date> The start date of the run. Default value: null.
--SORT <Boolean> If true, the output records are sorted by read name. Otherwise they are unsorted. Default
value: true. Possible values: {true, false}
--TAG_PER_MOLECULAR_INDEX <String>
The list of tags to store each molecular index. The number of tags should match the
number of molecular indexes. This argument may be specified 0 or more times. Default
value: null.
--THREE_PRIME_ADAPTER <String>For specifying adapters other than standard Illumina Default value: null.
--TILE_LIMIT <Integer> If set, process no more than this many tiles (used for debugging). Default value: null.
--TMP_DIR <File> One or more directories with space available to be used by this program for temporary
storage of working files This argument may be specified 0 or more times. Default value:
null.
--USE_JDK_DEFLATER,-use_jdk_deflater <Boolean>
Use the JDK Deflater instead of the Intel Deflater for writing compressed output Default
value: false. Possible values: {true, false}
--USE_JDK_INFLATER,-use_jdk_inflater <Boolean>
Use the JDK Inflater instead of the Intel Inflater for reading compressed input Default
value: false. Possible values: {true, false}
--VALIDATION_STRINGENCY <ValidationStringency>
Validation stringency for all SAM files read by this program. Setting stringency to
SILENT can improve performance when processing a BAM file in which variable-length data
(read, qualities, tags) do not otherwise need to be decoded. Default value: STRICT.
Possible values: {STRICT, LENIENT, SILENT}
--VERBOSITY <LogLevel> Control verbosity of logging. Default value: INFO. Possible values: {ERROR, WARNING,
INFO, DEBUG}
--version <Boolean> display the version number for this tool Default value: false. Possible values: {true,
false}
Advanced Arguments:
--showHidden <Boolean> display hidden arguments Default value: false. Possible values: {true, false}
The number of tags given in TAG_PER_MOLECULAR_INDEX does not match the number of molecular indexes in READ_STRUCTURE
USAGE: IlluminaBasecallsToSam [arguments]
Transforms raw Illumina sequencing data into an unmapped SAM, BAM or CRAM file.<p>The IlluminaBaseCallsToSam program
collects, demultiplexes, and sorts reads across all of the tiles of a lane via barcode to produce an unmapped SAM, BAM
or CRAM file. An unmapped BAM file is often referred to as a uBAM. All barcode, sample, and library data is provided
in the LIBRARY_PARAMS file. Note, this LIBRARY_PARAMS file should be formatted according to the specifications
indicated below. The following is an example of a properly formatted LIBRARY_PARAMS
file:</p>BARCODE_1 OUTPUT SAMPLE_ALIAS LIBRARY_NAME
AAAAAAAA SA_AAAAAAAA.bam SA_AAAAAAAA LN_AAAAAAAA
AAAAGAAG SA_AAAAGAAG.bam SA_AAAAGAAG LN_AAAAGAAG
AACAATGG SA_AACAATGG.bam SA_AACAATGG LN_AACAATGG
N SA_non_indexed.bam SA_non_indexed LN_NNNNNNNN
<p>The BARCODES_DIR file is produced by the <a
href='http://broadinstitute.github.io/picard/command-line-overview.html#ExtractIlluminaBarcodes'>ExtractIlluminaBarcodes</a>
tool for each lane of a flow cell.</p> <p>Barcode matching can be done inline without requiring barcodes files
generated by `ExtractIlluminaBarcode`. By setting MATCH_BARCODES_INLINE to true barcodes will be matched as they are
parsed and converted. Thisdoes not require BARCODES_DIR.</p> <h4>Usage example:</h4><pre>java -jar picard.jar
IlluminaBasecallsToSam \<br /> BASECALLS_DIR=/BaseCalls/ \<br /> LANE=001 \<br /> READ_STRUCTURE=25T8B25T
\<br /> RUN_BARCODE=run15 \<br /> IGNORE_UNEXPECTED_BARCODES=true \<br /> LIBRARY_PARAMS=library.params
</pre><hr />
Version:null
Required Arguments:
--BARCODE_PARAMS <File> Deprecated (use LIBRARY_PARAMS). Tab-separated file for creating all output SAM, BAM or
CRAM files for barcoded run with single IlluminaBasecallsToSam invocation. Columns are
BARCODE, OUTPUT, SAMPLE_ALIAS, and LIBRARY_NAME. Row with BARCODE=N is used to specify a
file for no barcode match Required. Cannot be used in conjunction with argument(s)
OUTPUT (O) SAMPLE_ALIAS (ALIAS) LIBRARY_NAME (LIB) LIBRARY_PARAMS
--BASECALLS_DIR,-B <File> The Illumina basecalls directory. Required.
--LANE,-L <Integer> Lane number. This can be specified multiple times. Reads with the same index in multiple
lanes will be added to the same output file. This argument must be specified at least
once. Required.
--LIBRARY_PARAMS <File> Tab-separated file for creating all output SAM, BAM or CRAM files for a lane with single
IlluminaBasecallsToSam invocation. The columns are OUTPUT, SAMPLE_ALIAS, and
LIBRARY_NAME, BARCODE_1, BARCODE_2 ... BARCODE_X where X = number of barcodes per cluster
(optional). Row with BARCODE_1 set to 'N' is used to specify a file for no barcode match.
You may also provide any 2 letter RG header attributes (excluding PU, CN, PL, and DT) as
columns in this file and the values for those columns will be inserted into the RG tag for
the SAM, BAM or CRAM file created for a given row. Required. Cannot be used in
conjunction with argument(s) OUTPUT (O) SAMPLE_ALIAS (ALIAS) LIBRARY_NAME (LIB)
BARCODE_PARAMS
--OUTPUT,-O <File> Deprecated (use LIBRARY_PARAMS). The output SAM, BAM or CRAM file. Format is determined
by extension. Required. Cannot be used in conjunction with argument(s) BARCODE_PARAMS
LIBRARY_PARAMS
--READ_STRUCTURE,-RS <String> A description of the logical structure of clusters in an Illumina Run, i.e. a description
of the structure IlluminaBasecallsToSam assumes the data to be in. It should consist of
integer/character pairs describing the number of cycles and the type of those cycles (B
for Sample Barcode, M for molecular barcode, T for Template, and S for skip). E.g. If the
input data consists of 80 base clusters and we provide a read structure of "28T8M8B8S28T"
then the sequence may be split up into four reads:
* read one with 28 cycles (bases) of template
* read two with 8 cycles (bases) of molecular barcode (ex. unique molecular barcode)
* read three with 8 cycles (bases) of sample barcode
* 8 cycles (bases) skipped.
* read four with 28 cycles (bases) of template
The skipped cycles would NOT be included in an output SAM/BAM file or in read groups
therein. Required.
--RUN_BARCODE <String> The barcode of the run. Prefixed to read names. Required.
--SAMPLE_ALIAS,-ALIAS <String>Deprecated (use LIBRARY_PARAMS). The name of the sequenced sample Required. Cannot be
used in conjunction with argument(s) BARCODE_PARAMS LIBRARY_PARAMS
--SEQUENCING_CENTER <String> The name of the sequencing center that produced the reads. Used to set the @RG->CN header
tag. Required.
Optional Arguments:
--ADAPTERS_TO_CHECK <IlluminaAdapterPair>
Which adapters to look for in the read. This argument may be specified 0 or more times.
Default value: [INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM]. Possible values:
{PAIRED_END, INDEXED, SINGLE_END, NEXTERA_V1, NEXTERA_V2, DUAL_INDEXED, FLUIDIGM,
TRUSEQ_SMALLRNA, ALTERNATIVE_SINGLE_END}
--APPLY_EAMSS_FILTER <Boolean>Apply EAMSS filtering to identify inappropriately quality scored bases towards the ends of
reads and convert their quality scores to Q2. Default value: true. Possible values:
{true, false}
--arguments_file <File> read one or more arguments files and add them to the command line This argument may be
specified 0 or more times. Default value: null.
--BARCODE_POPULATION_STRATEGY <PopulateBarcode>
When should the sample barcode (as read by the sequencer) be placed on the reads in the BC
tag? Default value: ORPHANS_ONLY. ORPHANS_ONLY (Put barcodes only into the records that
were not assigned to any declared barcode.)
INEXACT_MATCH (Put barcodes into records for which an exact match with a declared barcode
was not found.)
ALWAYS (Put barcodes into all the records.)
--BARCODES_DIR,-BCD <File> The barcodes directory with _barcode.txt files (generated by ExtractIlluminaBarcodes). If
not set, use BASECALLS_DIR. Default value: null.
--COMPRESS_OUTPUTS,-GZIP <Boolean>
Compress output FASTQ files using gzip and append a .gz extension to the file names.
Default value: false. Possible values: {true, false}
--COMPRESSION_LEVEL <Integer> Compression level for all compressed files created (e.g. BAM and VCF). Default value: 5.
--CREATE_INDEX <Boolean> Whether to create an index when writing VCF or coordinate sorted BAM output. Default
value: false. Possible values: {true, false}
--CREATE_MD5_FILE <Boolean> Whether to create an MD5 digest for any BAM or FASTQ files created. Default value:
false. Possible values: {true, false}
--DISTANCE_MODE <DistanceMetric>
The distance metric that should be used to compare the barcode-reads and the provided
barcodes for finding the best and second-best assignments. Default value: HAMMING.
HAMMING (Hamming distance: The n-th base in the read is compared against the n-th base in
the barcode. Unequal bases and low quality bases are considered mismatches. No-call
read-bases are not considered mismatches. )
LENIENT_HAMMING (Leniant Hamming distance: The n-th base in the read is compared against
the n-th base in the barcode. Unequal bases are considered mismatches. No-call read-bases,
or those with low quality are not considered mismatches.)
FREE (FREE Metric: A Levenshtein-like metric that performs a simple Smith-Waterman with
mismatch, gap open, and gap extend costs all equal to 1. Insertions or deletions at the
ends of the read or barcode do not count toward the distance. No-call read-bases, or those
with low quality are not considered mismatches.)
--FIRST_TILE <Integer> If set, this is the first tile to be processed (used for debugging). Note that tiles are
not processed in numerical order. Default value: null. Cannot be used in conjunction
with argument(s) PROCESS_SINGLE_TILE
--FIVE_PRIME_ADAPTER <String> For specifying adapters other than standard Illumina Default value: null.
--help,-h <Boolean> display the help message Default value: false. Possible values: {true, false}
--IGNORE_UNEXPECTED_BARCODES,-IGNORE_UNEXPECTED <Boolean>
Whether to ignore reads whose barcodes are not found in LIBRARY_PARAMS. Useful when
outputting SAM, BAM or CRAM files for only a subset of the barcodes in a lane. Default
value: false. Possible values: {true, false}
--INCLUDE_BARCODE_QUALITY <Boolean>
Should the barcode quality be included when the sample barcode is included? Default
value: false. Possible values: {true, false}
--INCLUDE_BC_IN_RG_TAG <Boolean>
Whether to include the barcode information in the @RG->BC header tag. Defaults to false
until included in the SAM spec. Default value: false. Possible values: {true, false}
--INCLUDE_NON_PF_READS,-NONPF <Boolean>
Whether to include non-PF reads Default value: true. Possible values: {true, false}
--INPUT_PARAMS_FILE <File> The input file that defines parameters for the program. This is the BARCODE_FILE for
`ExtractIlluminaBarcodes` or the MULTIPLEX_PARAMS or LIBRARY_PARAMS file for
`IlluminaBasecallsToFastq` or `IlluminaBasecallsToSam` Default value: null.
--LIBRARY_NAME,-LIB <String> Deprecated (use LIBRARY_PARAMS). The name of the sequenced library Default value: null.
Cannot be used in conjunction with argument(s) BARCODE_PARAMS LIBRARY_PARAMS
--MATCH_BARCODES_INLINE <Boolean>
If true, match barcodes on the fly. Otherwise parse the barcodes from the barcodes file.
Default value: false. Possible values: {true, false}
--MAX_MISMATCHES <Integer> Maximum mismatches for a barcode to be considered a match. Default value: 1.
--MAX_NO_CALLS <Integer> Maximum allowable number of no-calls in a barcode read before it is considered
unmatchable. Default value: 2.
--MAX_READS_IN_RAM_PER_TILE <Integer>
Configure SortingCollections to store this many records before spilling to disk. For an
indexed run, each SortingCollection gets this value/number of indices. Deprecated: use
`MAX_RECORDS_IN_RAM` Default value: -1.
--MAX_RECORDS_IN_RAM <Integer>When writing files that need to be sorted, this will specify the number of records stored
in RAM before spilling to disk. Increasing this number reduces the number of file handles
needed to sort the file, and increases the amount of RAM needed. Default value: 100.
--METRICS_FILE,-M <File> Per-barcode and per-lane metrics written to this file. Default value: null.
--MIN_MISMATCH_DELTA <Integer>Minimum difference between number of mismatches in the best and second best barcodes for a
barcode to be considered a match. Default value: 1.
--MINIMUM_BASE_QUALITY,-Q <Integer>
Minimum base quality. Any barcode bases falling below this quality will be considered a
mismatch even if the bases match. Default value: 0.
--MINIMUM_QUALITY <Integer> The minimum quality (after transforming 0s to 1s) expected from reads. If qualities are
lower than this value, an error is thrown. The default of 2 is what the Illumina's spec
describes as the minimum, but in practice the value has been observed lower. Default
value: 2.
--MOLECULAR_INDEX_BASE_QUALITY_TAG <String>
The tag to use to store any molecular index base qualities. If more than one molecular
index is found, their qualities will be concatenated and stored here (.i.e. the number of
"M" operators in the READ_STRUCTURE) Default value: QX.
--MOLECULAR_INDEX_TAG <String>The tag to use to store any molecular indexes. If more than one molecular index is found,
they will be concatenated and stored here. Default value: RX.
--NUM_PROCESSORS <Integer> The number of threads to run in parallel. If NUM_PROCESSORS = 0, number of cores is
automatically set to the number of cores available on the machine. If NUM_PROCESSORS < 0,
then the number of cores used will be the number available on the machine less
NUM_PROCESSORS. Default value: 0.
--PLATFORM <String> The name of the sequencing technology that produced the read. Default value: ILLUMINA.
--PROCESS_SINGLE_TILE <Integer>
If set, process only the tile number given and prepend the tile number to the output file
name. Default value: null. Cannot be used in conjunction with argument(s) FIRST_TILE
--QUIET <Boolean> Whether to suppress job-summary info on System.err. Default value: false. Possible
values: {true, false}
--READ_GROUP_ID,-RG <String> ID used to link RG header record with RG tag in SAM record. If these are unique in SAM
files that get merged, merge performance is better. If not specified, READ_GROUP_ID will
be set to <first 5 chars of RUN_BARCODE>.<LANE> . Default value: null.
--REFERENCE_SEQUENCE,-R <PicardHtsPath>
Reference sequence file. Default value: null.
--RUN_START_DATE <Date> The start date of the run. Default value: null.
--SORT <Boolean> If true, the output records are sorted by read name. Otherwise they are unsorted. Default
value: true. Possible values: {true, false}
--TAG_PER_MOLECULAR_INDEX <String>
The list of tags to store each molecular index. The number of tags should match the
number of molecular indexes. This argument may be specified 0 or more times. Default
value: null.
--THREE_PRIME_ADAPTER <String>For specifying adapters other than standard Illumina Default value: null.
--TILE_LIMIT <Integer> If set, process no more than this many tiles (used for debugging). Default value: null.
--TMP_DIR <File> One or more directories with space available to be used by this program for temporary
storage of working files This argument may be specified 0 or more times. Default value:
null.
--USE_JDK_DEFLATER,-use_jdk_deflater <Boolean>
Use the JDK Deflater instead of the Intel Deflater for writing compressed output Default
value: false. Possible values: {true, false}
--USE_JDK_INFLATER,-use_jdk_inflater <Boolean>
Use the JDK Inflater instead of the Intel Inflater for reading compressed input Default
value: false. Possible values: {true, false}
--VALIDATION_STRINGENCY <ValidationStringency>
Validation stringency for all SAM files read by this program. Setting stringency to
SILENT can improve performance when processing a BAM file in which variable-length data
(read, qualities, tags) do not otherwise need to be decoded. Default value: STRICT.
Possible values: {STRICT, LENIENT, SILENT}
--VERBOSITY <LogLevel> Control verbosity of logging. Default value: INFO. Possible values: {ERROR, WARNING,
INFO, DEBUG}
--version <Boolean> display the version number for this tool Default value: false. Possible values: {true,
false}
Advanced Arguments:
--showHidden <Boolean> display hidden arguments Default value: false. Possible values: {true, false}
The number of tags given in TAG_PER_MOLECULAR_INDEX does not match the number of molecular indexes in READ_STRUCTURE
USAGE: IlluminaBasecallsToSam [arguments]
Transforms raw Illumina sequencing data into an unmapped SAM, BAM or CRAM file.<p>The IlluminaBaseCallsToSam program
collects, demultiplexes, and sorts reads across all of the tiles of a lane via barcode to produce an unmapped SAM, BAM
or CRAM file. An unmapped BAM file is often referred to as a uBAM. All barcode, sample, and library data is provided
in the LIBRARY_PARAMS file. Note, this LIBRARY_PARAMS file should be formatted according to the specifications
indicated below. The following is an example of a properly formatted LIBRARY_PARAMS
file:</p>BARCODE_1 OUTPUT SAMPLE_ALIAS LIBRARY_NAME
AAAAAAAA SA_AAAAAAAA.bam SA_AAAAAAAA LN_AAAAAAAA
AAAAGAAG SA_AAAAGAAG.bam SA_AAAAGAAG LN_AAAAGAAG
AACAATGG SA_AACAATGG.bam SA_AACAATGG LN_AACAATGG
N SA_non_indexed.bam SA_non_indexed LN_NNNNNNNN
<p>The BARCODES_DIR file is produced by the <a
href='http://broadinstitute.github.io/picard/command-line-overview.html#ExtractIlluminaBarcodes'>ExtractIlluminaBarcodes</a>
tool for each lane of a flow cell.</p> <p>Barcode matching can be done inline without requiring barcodes files
generated by `ExtractIlluminaBarcode`. By setting MATCH_BARCODES_INLINE to true barcodes will be matched as they are
parsed and converted. Thisdoes not require BARCODES_DIR.</p> <h4>Usage example:</h4><pre>java -jar picard.jar
IlluminaBasecallsToSam \<br /> BASECALLS_DIR=/BaseCalls/ \<br /> LANE=001 \<br /> READ_STRUCTURE=25T8B25T
\<br /> RUN_BARCODE=run15 \<br /> IGNORE_UNEXPECTED_BARCODES=true \<br /> LIBRARY_PARAMS=library.params
</pre><hr />
Version:null
Required Arguments:
--BARCODE_PARAMS <File> Deprecated (use LIBRARY_PARAMS). Tab-separated file for creating all output SAM, BAM or
CRAM files for barcoded run with single IlluminaBasecallsToSam invocation. Columns are
BARCODE, OUTPUT, SAMPLE_ALIAS, and LIBRARY_NAME. Row with BARCODE=N is used to specify a
file for no barcode match Required. Cannot be used in conjunction with argument(s)
OUTPUT (O) SAMPLE_ALIAS (ALIAS) LIBRARY_NAME (LIB) LIBRARY_PARAMS
--BASECALLS_DIR,-B <File> The Illumina basecalls directory. Required.
--LANE,-L <Integer> Lane number. This can be specified multiple times. Reads with the same index in multiple
lanes will be added to the same output file. This argument must be specified at least
once. Required.
--LIBRARY_PARAMS <File> Tab-separated file for creating all output SAM, BAM or CRAM files for a lane with single
IlluminaBasecallsToSam invocation. The columns are OUTPUT, SAMPLE_ALIAS, and
LIBRARY_NAME, BARCODE_1, BARCODE_2 ... BARCODE_X where X = number of barcodes per cluster
(optional). Row with BARCODE_1 set to 'N' is used to specify a file for no barcode match.
You may also provide any 2 letter RG header attributes (excluding PU, CN, PL, and DT) as
columns in this file and the values for those columns will be inserted into the RG tag for
the SAM, BAM or CRAM file created for a given row. Required. Cannot be used in
conjunction with argument(s) OUTPUT (O) SAMPLE_ALIAS (ALIAS) LIBRARY_NAME (LIB)
BARCODE_PARAMS
--OUTPUT,-O <File> Deprecated (use LIBRARY_PARAMS). The output SAM, BAM or CRAM file. Format is determined
by extension. Required. Cannot be used in conjunction with argument(s) BARCODE_PARAMS
LIBRARY_PARAMS
--READ_STRUCTURE,-RS <String> A description of the logical structure of clusters in an Illumina Run, i.e. a description
of the structure IlluminaBasecallsToSam assumes the data to be in. It should consist of
integer/character pairs describing the number of cycles and the type of those cycles (B
for Sample Barcode, M for molecular barcode, T for Template, and S for skip). E.g. If the
input data consists of 80 base clusters and we provide a read structure of "28T8M8B8S28T"
then the sequence may be split up into four reads:
* read one with 28 cycles (bases) of template
* read two with 8 cycles (bases) of molecular barcode (ex. unique molecular barcode)
* read three with 8 cycles (bases) of sample barcode
* 8 cycles (bases) skipped.
* read four with 28 cycles (bases) of template
The skipped cycles would NOT be included in an output SAM/BAM file or in read groups
therein. Required.
--RUN_BARCODE <String> The barcode of the run. Prefixed to read names. Required.
--SAMPLE_ALIAS,-ALIAS <String>Deprecated (use LIBRARY_PARAMS). The name of the sequenced sample Required. Cannot be
used in conjunction with argument(s) BARCODE_PARAMS LIBRARY_PARAMS
--SEQUENCING_CENTER <String> The name of the sequencing center that produced the reads. Used to set the @RG->CN header
tag. Required.
Optional Arguments:
--ADAPTERS_TO_CHECK <IlluminaAdapterPair>
Which adapters to look for in the read. This argument may be specified 0 or more times.
Default value: [INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM]. Possible values:
{PAIRED_END, INDEXED, SINGLE_END, NEXTERA_V1, NEXTERA_V2, DUAL_INDEXED, FLUIDIGM,
TRUSEQ_SMALLRNA, ALTERNATIVE_SINGLE_END}
--APPLY_EAMSS_FILTER <Boolean>Apply EAMSS filtering to identify inappropriately quality scored bases towards the ends of
reads and convert their quality scores to Q2. Default value: true. Possible values:
{true, false}
--arguments_file <File> read one or more arguments files and add them to the command line This argument may be
specified 0 or more times. Default value: null.
--BARCODE_POPULATION_STRATEGY <PopulateBarcode>
When should the sample barcode (as read by the sequencer) be placed on the reads in the BC
tag? Default value: ORPHANS_ONLY. ORPHANS_ONLY (Put barcodes only into the records that
were not assigned to any declared barcode.)
INEXACT_MATCH (Put barcodes into records for which an exact match with a declared barcode
was not found.)
ALWAYS (Put barcodes into all the records.)
--BARCODES_DIR,-BCD <File> The barcodes directory with _barcode.txt files (generated by ExtractIlluminaBarcodes). If
not set, use BASECALLS_DIR. Default value: null.
--COMPRESS_OUTPUTS,-GZIP <Boolean>
Compress output FASTQ files using gzip and append a .gz extension to the file names.
Default value: false. Possible values: {true, false}
--COMPRESSION_LEVEL <Integer> Compression level for all compressed files created (e.g. BAM and VCF). Default value: 5.
--CREATE_INDEX <Boolean> Whether to create an index when writing VCF or coordinate sorted BAM output. Default
value: false. Possible values: {true, false}
--CREATE_MD5_FILE <Boolean> Whether to create an MD5 digest for any BAM or FASTQ files created. Default value:
false. Possible values: {true, false}
--DISTANCE_MODE <DistanceMetric>
The distance metric that should be used to compare the barcode-reads and the provided
barcodes for finding the best and second-best assignments. Default value: HAMMING.
HAMMING (Hamming distance: The n-th base in the read is compared against the n-th base in
the barcode. Unequal bases and low quality bases are considered mismatches. No-call
read-bases are not considered mismatches. )
LENIENT_HAMMING (Leniant Hamming distance: The n-th base in the read is compared against
the n-th base in the barcode. Unequal bases are considered mismatches. No-call read-bases,
or those with low quality are not considered mismatches.)
FREE (FREE Metric: A Levenshtein-like metric that performs a simple Smith-Waterman with
mismatch, gap open, and gap extend costs all equal to 1. Insertions or deletions at the
ends of the read or barcode do not count toward the distance. No-call read-bases, or those
with low quality are not considered mismatches.)
--FIRST_TILE <Integer> If set, this is the first tile to be processed (used for debugging). Note that tiles are
not processed in numerical order. Default value: null. Cannot be used in conjunction
with argument(s) PROCESS_SINGLE_TILE
--FIVE_PRIME_ADAPTER <String> For specifying adapters other than standard Illumina Default value: null.
--help,-h <Boolean> display the help message Default value: false. Possible values: {true, false}
--IGNORE_UNEXPECTED_BARCODES,-IGNORE_UNEXPECTED <Boolean>
Whether to ignore reads whose barcodes are not found in LIBRARY_PARAMS. Useful when
outputting SAM, BAM or CRAM files for only a subset of the barcodes in a lane. Default
value: false. Possible values: {true, false}
--INCLUDE_BARCODE_QUALITY <Boolean>
Should the barcode quality be included when the sample barcode is included? Default
value: false. Possible values: {true, false}
--INCLUDE_BC_IN_RG_TAG <Boolean>
Whether to include the barcode information in the @RG->BC header tag. Defaults to false
until included in the SAM spec. Default value: false. Possible values: {true, false}
--INCLUDE_NON_PF_READS,-NONPF <Boolean>
Whether to include non-PF reads Default value: true. Possible values: {true, false}
--INPUT_PARAMS_FILE <File> The input file that defines parameters for the program. This is the BARCODE_FILE for
`ExtractIlluminaBarcodes` or the MULTIPLEX_PARAMS or LIBRARY_PARAMS file for
`IlluminaBasecallsToFastq` or `IlluminaBasecallsToSam` Default value: null.
--LIBRARY_NAME,-LIB <String> Deprecated (use LIBRARY_PARAMS). The name of the sequenced library Default value: null.
Cannot be used in conjunction with argument(s) BARCODE_PARAMS LIBRARY_PARAMS
--MATCH_BARCODES_INLINE <Boolean>
If true, match barcodes on the fly. Otherwise parse the barcodes from the barcodes file.
Default value: false. Possible values: {true, false}
--MAX_MISMATCHES <Integer> Maximum mismatches for a barcode to be considered a match. Default value: 1.
--MAX_NO_CALLS <Integer> Maximum allowable number of no-calls in a barcode read before it is considered
unmatchable. Default value: 2.
--MAX_READS_IN_RAM_PER_TILE <Integer>
Configure SortingCollections to store this many records before spilling to disk. For an
indexed run, each SortingCollection gets this value/number of indices. Deprecated: use
`MAX_RECORDS_IN_RAM` Default value: -1.
--MAX_RECORDS_IN_RAM <Integer>When writing files that need to be sorted, this will specify the number of records stored
in RAM before spilling to disk. Increasing this number reduces the number of file handles
needed to sort the file, and increases the amount of RAM needed. Default value: 100.
--METRICS_FILE,-M <File> Per-barcode and per-lane metrics written to this file. Default value: null.
--MIN_MISMATCH_DELTA <Integer>Minimum difference between number of mismatches in the best and second best barcodes for a
barcode to be considered a match. Default value: 1.
--MINIMUM_BASE_QUALITY,-Q <Integer>
Minimum base quality. Any barcode bases falling below this quality will be considered a
mismatch even if the bases match. Default value: 0.
--MINIMUM_QUALITY <Integer> The minimum quality (after transforming 0s to 1s) expected from reads. If qualities are
lower than this value, an error is thrown. The default of 2 is what the Illumina's spec
describes as the minimum, but in practice the value has been observed lower. Default
value: 2.
--MOLECULAR_INDEX_BASE_QUALITY_TAG <String>
The tag to use to store any molecular index base qualities. If more than one molecular
index is found, their qualities will be concatenated and stored here (.i.e. the number of
"M" operators in the READ_STRUCTURE) Default value: QX.
--MOLECULAR_INDEX_TAG <String>The tag to use to store any molecular indexes. If more than one molecular index is found,
they will be concatenated and stored here. Default value: RX.
--NUM_PROCESSORS <Integer> The number of threads to run in parallel. If NUM_PROCESSORS = 0, number of cores is
automatically set to the number of cores available on the machine. If NUM_PROCESSORS < 0,
then the number of cores used will be the number available on the machine less
NUM_PROCESSORS. Default value: 0.
--PLATFORM <String> The name of the sequencing technology that produced the read. Default value: ILLUMINA.
--PROCESS_SINGLE_TILE <Integer>
If set, process only the tile number given and prepend the tile number to the output file
name. Default value: null. Cannot be used in conjunction with argument(s) FIRST_TILE
--QUIET <Boolean> Whether to suppress job-summary info on System.err. Default value: false. Possible
values: {true, false}
--READ_GROUP_ID,-RG <String> ID used to link RG header record with RG tag in SAM record. If these are unique in SAM
files that get merged, merge performance is better. If not specified, READ_GROUP_ID will
be set to <first 5 chars of RUN_BARCODE>.<LANE> . Default value: null.
--REFERENCE_SEQUENCE,-R <PicardHtsPath>
Reference sequence file. Default value: null.
--RUN_START_DATE <Date> The start date of the run. Default value: null.
--SORT <Boolean> If true, the output records are sorted by read name. Otherwise they are unsorted. Default
value: true. Possible values: {true, false}
--TAG_PER_MOLECULAR_INDEX <String>
The list of tags to store each molecular index. The number of tags should match the
number of molecular indexes. This argument may be specified 0 or more times. Default
value: null.
--THREE_PRIME_ADAPTER <String>For specifying adapters other than standard Illumina Default value: null.
--TILE_LIMIT <Integer> If set, process no more than this many tiles (used for debugging). Default value: null.
--TMP_DIR <File> One or more directories with space available to be used by this program for temporary
storage of working files This argument may be specified 0 or more times. Default value:
null.
--USE_JDK_DEFLATER,-use_jdk_deflater <Boolean>
Use the JDK Deflater instead of the Intel Deflater for writing compressed output Default
value: false. Possible values: {true, false}
--USE_JDK_INFLATER,-use_jdk_inflater <Boolean>
Use the JDK Inflater instead of the Intel Inflater for reading compressed input Default
value: false. Possible values: {true, false}
--VALIDATION_STRINGENCY <ValidationStringency>
Validation stringency for all SAM files read by this program. Setting stringency to
SILENT can improve performance when processing a BAM file in which variable-length data
(read, qualities, tags) do not otherwise need to be decoded. Default value: STRICT.
Possible values: {STRICT, LENIENT, SILENT}
--VERBOSITY <LogLevel> Control verbosity of logging. Default value: INFO. Possible values: {ERROR, WARNING,
INFO, DEBUG}
--version <Boolean> display the version number for this tool Default value: false. Possible values: {true,
false}
Advanced Arguments:
--showHidden <Boolean> display hidden arguments Default value: false. Possible values: {true, false}
The number of tags given in TAG_PER_MOLECULAR_INDEX does not match the number of molecular indexes in READ_STRUCTURE
[Thu Apr 24 13:01:37 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/molecularBarcodeTest.4016709985263654362.sam --RUN_BARCODE HiMom --SAMPLE_ALIAS HiDad --LIBRARY_NAME Hello, World --SEQUENCING_CENTER BI --TAG_PER_MOLECULAR_INDEX ZA --TAG_PER_MOLECULAR_INDEX ZB --TAG_PER_MOLECULAR_INDEX ZC --TAG_PER_MOLECULAR_INDEX ZD --SORT false --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25S2M2M2M2M25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --PLATFORM ILLUMINA --INCLUDE_BC_IN_RG_TAG false --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:37 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:01:37 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S2M2M2M2M25T
[Thu Apr 24 13:01:37 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:37 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/molecularBarcodeTest.16114035973286384535.sam --RUN_BARCODE HiMom --SAMPLE_ALIAS HiDad --LIBRARY_NAME Hello, World --SEQUENCING_CENTER BI --TAG_PER_MOLECULAR_INDEX ZA --TAG_PER_MOLECULAR_INDEX ZB --TAG_PER_MOLECULAR_INDEX ZC --TAG_PER_MOLECULAR_INDEX ZD --SORT false --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25S2M2M2M2M25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --PLATFORM ILLUMINA --INCLUDE_BC_IN_RG_TAG false --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:37 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:01:37 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S2M2M2M2M25T
[Thu Apr 24 13:01:37 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:37 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/molecularBarcodeTest.7644269273939420010.sam --RUN_BARCODE HiMom --SAMPLE_ALIAS HiDad --LIBRARY_NAME Hello, World --SEQUENCING_CENTER BI --TAG_PER_MOLECULAR_INDEX ZA --TAG_PER_MOLECULAR_INDEX ZB --TAG_PER_MOLECULAR_INDEX ZC --TAG_PER_MOLECULAR_INDEX ZD --SORT true --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25S2M2M2M2M25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --PLATFORM ILLUMINA --INCLUDE_BC_IN_RG_TAG false --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:37 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:01:37 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S2M2M2M2M25T
INFO 2025-04-24 13:01:37 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:01:37 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:01:37 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:01:37 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:01:37 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:01:37 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:01:37 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:01:37 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:01:37 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:37 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/molecularBarcodeTest.5870655542887138838.sam --RUN_BARCODE HiMom --SAMPLE_ALIAS HiDad --LIBRARY_NAME Hello, World --SEQUENCING_CENTER BI --TAG_PER_MOLECULAR_INDEX ZA --TAG_PER_MOLECULAR_INDEX ZB --TAG_PER_MOLECULAR_INDEX ZC --TAG_PER_MOLECULAR_INDEX ZD --SORT true --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25S2M2M2M2M25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --PLATFORM ILLUMINA --INCLUDE_BC_IN_RG_TAG false --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:37 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:01:37 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S2M2M2M2M25T
INFO 2025-04-24 13:01:37 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:01:37 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:01:37 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:01:38 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:01:38 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:01:38 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:01:38 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:01:38 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:01:38 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:38 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/molecularBarcodeTest.10148922089055257472.sam --RUN_BARCODE HiMom --SAMPLE_ALIAS HiDad --LIBRARY_NAME Hello, World --SEQUENCING_CENTER BI --FIRST_TILE 1201 --TILE_LIMIT 1 --SORT false --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25S8S25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --PLATFORM ILLUMINA --INCLUDE_BC_IN_RG_TAG false --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:38 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:01:38 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S8S25T
[Thu Apr 24 13:01:38 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:38 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/molecularBarcodeTest.3136589366349032527.sam --RUN_BARCODE HiMom --SAMPLE_ALIAS HiDad --LIBRARY_NAME Hello, World --SEQUENCING_CENTER BI --FIRST_TILE 1201 --TILE_LIMIT 1 --SORT false --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25S8S25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --PLATFORM ILLUMINA --INCLUDE_BC_IN_RG_TAG false --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:38 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:01:38 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S8S25T
[Thu Apr 24 13:01:38 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:38 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/molecularBarcodeTest.6235899133253571232.sam --RUN_BARCODE HiMom --SAMPLE_ALIAS HiDad --LIBRARY_NAME Hello, World --SEQUENCING_CENTER BI --FIRST_TILE 1201 --TILE_LIMIT 1 --SORT true --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25S8S25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --PLATFORM ILLUMINA --INCLUDE_BC_IN_RG_TAG false --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:38 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:01:38 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S8S25T
INFO 2025-04-24 13:01:38 SortedBasecallsConverter Tile Read Executor - Queueing: 1 TileProcessor jobs
INFO 2025-04-24 13:01:38 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:01:38 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:01:38 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
[Thu Apr 24 13:01:38 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:38 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/molecularBarcodeTest.12666407578305925504.sam --RUN_BARCODE HiMom --SAMPLE_ALIAS HiDad --LIBRARY_NAME Hello, World --SEQUENCING_CENTER BI --FIRST_TILE 1201 --TILE_LIMIT 1 --SORT true --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25S8S25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --PLATFORM ILLUMINA --INCLUDE_BC_IN_RG_TAG false --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:38 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:01:38 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S8S25T
INFO 2025-04-24 13:01:38 SortedBasecallsConverter Tile Read Executor - Queueing: 1 TileProcessor jobs
INFO 2025-04-24 13:01:38 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:01:38 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:01:38 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
[Thu Apr 24 13:01:38 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:38 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG true --LIBRARY_PARAMS /tmp/multiplexedBarcode.true2001600063436441031/library.params --BARCODE_POPULATION_STRATEGY ALWAYS --INCLUDE_BARCODE_QUALITY false --SORT true --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25T8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.10042413344136203265.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:38 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:01:38 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B25T
INFO 2025-04-24 13:01:38 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:01:38 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:01:38 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:01:40 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:01:40 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:01:42 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:01:42 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:01:44 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:01:44 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:44 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG true --LIBRARY_PARAMS /tmp/multiplexedBarcode.true9024548565955963476/library.params --BARCODE_POPULATION_STRATEGY ALWAYS --INCLUDE_BARCODE_QUALITY false --SORT true --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25T8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.17057060115581899387.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:44 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:01:44 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B25T
INFO 2025-04-24 13:01:44 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:01:44 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:01:44 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:01:46 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:01:46 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:01:47 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:01:47 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:01:49 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:01:49 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:50 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG true --LIBRARY_PARAMS /tmp/multiplexedBarcode.false6905080106465150585/library.params --BARCODE_POPULATION_STRATEGY ALWAYS --INCLUDE_BARCODE_QUALITY false --SORT false --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25T8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.7887023283143690541.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:50 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:01:50 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B25T
[Thu Apr 24 13:01:50 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:50 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG true --LIBRARY_PARAMS /tmp/multiplexedBarcode.false13999628831041646683/library.params --BARCODE_POPULATION_STRATEGY ALWAYS --INCLUDE_BARCODE_QUALITY false --SORT false --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25T8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.1200647273407795828.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:50 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:01:50 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B25T
[Thu Apr 24 13:01:50 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:50 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/multiplexedBarcode.true11600229583814505812/library.params --BARCODE_POPULATION_STRATEGY INEXACT_MATCH --INCLUDE_BARCODE_QUALITY true --SORT true --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25T8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.5371106721791106340.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:50 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:01:50 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B25T
INFO 2025-04-24 13:01:50 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:01:50 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:01:50 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:01:51 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:01:51 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:01:53 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:01:53 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:01:55 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:01:55 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:55 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/multiplexedBarcode.true7515024204759841068/library.params --BARCODE_POPULATION_STRATEGY INEXACT_MATCH --INCLUDE_BARCODE_QUALITY true --SORT true --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25T8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.460259059189354990.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:55 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:01:55 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B25T
INFO 2025-04-24 13:01:55 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:01:55 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:01:55 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:01:57 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:01:57 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:01:59 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:01:59 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:02:01 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:02:01 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:02:01 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/multiplexedBarcode.false5505897285293703322/library.params --BARCODE_POPULATION_STRATEGY INEXACT_MATCH --INCLUDE_BARCODE_QUALITY true --SORT false --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25T8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.3136319840282252417.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:02:01 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:02:01 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B25T
[Thu Apr 24 13:02:01 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:02:01 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/multiplexedBarcode.false10962347075081650946/library.params --BARCODE_POPULATION_STRATEGY INEXACT_MATCH --INCLUDE_BARCODE_QUALITY true --SORT false --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25T8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.4858022639284059200.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:02:01 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:02:01 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B25T
[Thu Apr 24 13:02:01 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:02:01 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG true --LIBRARY_PARAMS /tmp/multiplexedBarcode.true9364373543679487466/library.params --BARCODE_POPULATION_STRATEGY ALWAYS --INCLUDE_BARCODE_QUALITY true --SORT true --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25T8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.2711288859035778335.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:02:01 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:02:01 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B25T
INFO 2025-04-24 13:02:01 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:02:01 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:02:01 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:02:03 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:02:03 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:02:05 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:02:05 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:02:07 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:02:07 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:02:07 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG true --LIBRARY_PARAMS /tmp/multiplexedBarcode.true2653826361149636210/library.params --BARCODE_POPULATION_STRATEGY ALWAYS --INCLUDE_BARCODE_QUALITY true --SORT true --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25T8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.3043580049165404891.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:02:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:02:07 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B25T
INFO 2025-04-24 13:02:07 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:02:07 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:02:07 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:02:09 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:02:09 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:02:10 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:02:10 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:02:12 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:02:12 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:02:13 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG true --LIBRARY_PARAMS /tmp/multiplexedBarcode.false9532444578452445395/library.params --BARCODE_POPULATION_STRATEGY ALWAYS --INCLUDE_BARCODE_QUALITY true --SORT false --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25T8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.10800591525467913286.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:02:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:02:13 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B25T
[Thu Apr 24 13:02:13 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:02:13 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG true --LIBRARY_PARAMS /tmp/multiplexedBarcode.false458779951797228193/library.params --BARCODE_POPULATION_STRATEGY ALWAYS --INCLUDE_BARCODE_QUALITY true --SORT false --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25T8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.8647052976169933492.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:02:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:02:13 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B25T
[Thu Apr 24 13:02:13 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:02:13 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/multiplexedBarcode.true17800618808950370292/library.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT true --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25T8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.14396057542685948433.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:02:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:02:13 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B25T
INFO 2025-04-24 13:02:13 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:02:13 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:02:13 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:02:14 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:02:14 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:02:16 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:02:16 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:02:18 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:02:18 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:02:18 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/multiplexedBarcode.true8971047244174447575/library.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT true --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25T8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.16325624598709862361.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:02:18 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:02:18 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B25T
INFO 2025-04-24 13:02:18 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:02:18 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:02:18 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:02:20 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:02:20 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:02:22 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:02:22 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:02:24 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:02:24 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:02:24 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/multiplexedBarcode.false5976498135617793675/library.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT false --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25T8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.5681061104750841838.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:02:24 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:02:24 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B25T
[Thu Apr 24 13:02:24 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:02:24 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/multiplexedBarcode.false11192952578589725603/library.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT false --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25T8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.7510668036830839157.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:02:24 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:02:24 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B25T
[Thu Apr 24 13:02:24 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:02:24 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/nonBarcodedDescriptionNonBI.4909337211424700596.sam --RUN_BARCODE HiMom --SAMPLE_ALIAS HiDad --LIBRARY_NAME Hello, World --SEQUENCING_CENTER TEST_CENTER123 --SORT false --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25S8S25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --PLATFORM ILLUMINA --INCLUDE_BC_IN_RG_TAG false --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:02:24 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:02:24 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S8S25T
[Thu Apr 24 13:02:24 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:02:24 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/nonBarcodedDescriptionNonBI.12112775871090365257.sam --RUN_BARCODE HiMom --SAMPLE_ALIAS HiDad --LIBRARY_NAME Hello, World --SEQUENCING_CENTER TEST_CENTER123 --SORT false --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25S8S25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --PLATFORM ILLUMINA --INCLUDE_BC_IN_RG_TAG false --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:02:24 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:02:24 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S8S25T
[Thu Apr 24 13:02:24 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:02:24 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/nonBarcodedDescriptionNonBI.11861589978438900588.sam --RUN_BARCODE HiMom --SAMPLE_ALIAS HiDad --LIBRARY_NAME Hello, World --SEQUENCING_CENTER TEST_CENTER123 --SORT true --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25S8S25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --PLATFORM ILLUMINA --INCLUDE_BC_IN_RG_TAG false --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:02:24 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:02:24 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S8S25T
INFO 2025-04-24 13:02:24 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:02:24 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:02:24 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:02:24 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:02:24 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:02:25 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:02:25 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:02:25 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:02:25 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:02:25 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/nonBarcodedDescriptionNonBI.14602824834139533156.sam --RUN_BARCODE HiMom --SAMPLE_ALIAS HiDad --LIBRARY_NAME Hello, World --SEQUENCING_CENTER TEST_CENTER123 --SORT true --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25S8S25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --PLATFORM ILLUMINA --INCLUDE_BC_IN_RG_TAG false --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:02:25 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:02:25 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S8S25T
INFO 2025-04-24 13:02:25 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:02:25 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:02:25 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:02:25 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:02:25 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:02:25 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:02:25 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:02:25 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:02:25 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:02:25 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/multiplexedBarcode.true5538484519333807313/library.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT true --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25T8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.15945955620905132537.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:02:25 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:02:25 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B25T
INFO 2025-04-24 13:02:25 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:02:25 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:02:25 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:02:27 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:02:27 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:02:29 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:02:29 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:02:31 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:02:31 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:02:31 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/multiplexedBarcode.true7682024679289596465/library.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT true --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25T8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.6767508514293102909.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:02:31 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:02:31 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B25T
INFO 2025-04-24 13:02:31 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:02:31 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:02:31 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:02:33 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:02:33 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:02:34 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:02:34 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:02:36 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:02:36 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:02:36 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/multiplexedBarcode.false13669158238632644971/library.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT false --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25T8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.13472406087583085629.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:02:36 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:02:36 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B25T
[Thu Apr 24 13:02:36 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:02:37 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/multiplexedBarcode.false8504987393868890336/library.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT false --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25T8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.11036017164115789853.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:02:37 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:02:37 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B25T
[Thu Apr 24 13:02:37 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:02:37 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/multiplexedBarcode.true16463604743845263223/library.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT true --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25T8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.9752529162657735795.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:02:37 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:02:37 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B25T
INFO 2025-04-24 13:02:37 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:02:37 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:02:37 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:02:38 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:02:38 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:02:40 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:02:40 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:02:42 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:02:42 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:02:42 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/multiplexedBarcode.true14312942316624902938/library.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT true --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25T8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.6620299273267599953.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:02:42 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:02:42 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B25T
INFO 2025-04-24 13:02:42 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:02:42 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:02:42 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:02:44 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:02:44 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:02:46 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:02:46 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:02:48 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:02:48 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:02:48 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/multiplexedBarcode.false4775667630031316102/library.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT false --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25T8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.11327515492677985900.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:02:48 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:02:48 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B25T
[Thu Apr 24 13:02:48 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:02:48 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/multiplexedBarcode.false3609282935905105478/library.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT false --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25T8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.14708403729838629459.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:02:48 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:02:48 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B25T
[Thu Apr 24 13:02:48 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:02:48 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/multiplexedBarcode.true11316365778679103295/library.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT true --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25T8B4M21T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.1354442675191092338.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:02:48 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:02:48 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B4M21T
INFO 2025-04-24 13:02:48 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:02:48 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:02:48 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:02:50 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:02:50 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:02:52 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:02:52 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:02:54 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:02:54 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:02:54 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/multiplexedBarcode.true5618908561254388643/library.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT true --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25T8B4M21T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.9373182736262677053.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:02:54 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:02:54 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B4M21T
INFO 2025-04-24 13:02:54 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:02:54 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:02:54 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:02:56 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:02:56 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:02:57 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:02:57 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:02:59 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:02:59 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:02:59 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/multiplexedBarcode.false990391011205459613/library.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT false --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25T8B4M21T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.12880651135247826722.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:02:59 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:02:59 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B4M21T
[Thu Apr 24 13:02:59 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:02:59 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/multiplexedBarcode.false13472469942507624093/library.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT false --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25T8B4M21T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.11026166239565929259.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:02:59 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:02:59 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B4M21T
[Thu Apr 24 13:02:59 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:00 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/multiplexedBarcode2.true7748039415316510178/library.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT true --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25T8B4M4M17T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.545324526763313356.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:00 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:03:00 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B4M4M17T
INFO 2025-04-24 13:03:00 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:03:00 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:03:00 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:03:01 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:03:01 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:03:03 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:03:03 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:03:05 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:03:05 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:05 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/multiplexedBarcode2.true7356124566990293615/library.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT true --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25T8B4M4M17T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.18112586606186339045.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:03:05 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B4M4M17T
INFO 2025-04-24 13:03:05 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:03:05 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:03:05 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:03:07 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:03:07 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:03:09 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:03:09 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:03:11 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:03:11 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:11 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/multiplexedBarcode2.false2970445549027173513/library.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT false --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25T8B4M4M17T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.2394977171437048934.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:11 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:03:11 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B4M4M17T
[Thu Apr 24 13:03:11 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:11 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/multiplexedBarcode2.false11977729736240488009/library.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT false --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25T8B4M4M17T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.3472679427146636490.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:11 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:03:11 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B4M4M17T
[Thu Apr 24 13:03:11 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:11 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/singleBarcodeAltName.true8978056608523746724/multiplexed_positive_rgtags.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT true --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25T8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.15376926466417561870.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:11 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:03:11 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B25T
INFO 2025-04-24 13:03:11 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:03:11 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:03:11 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:03:13 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:03:13 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:03:15 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:03:15 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:03:17 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:03:17 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:17 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/singleBarcodeAltName.true2210266309311897865/multiplexed_positive_rgtags.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT true --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25T8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.13830673895542965234.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:17 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:03:17 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B25T
INFO 2025-04-24 13:03:17 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:03:17 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:03:17 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:03:18 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:03:18 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:03:20 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:03:20 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:03:22 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:03:22 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:22 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/singleBarcodeAltName.false177443159859996414/multiplexed_positive_rgtags.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT false --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25T8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.15718206128167286257.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:22 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:03:22 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B25T
[Thu Apr 24 13:03:22 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:22 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/singleBarcodeAltName.false9132117173965714032/multiplexed_positive_rgtags.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT false --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25T8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.16759984361746698140.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:22 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:03:22 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B25T
[Thu Apr 24 13:03:22 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:23 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/dualBarcode.true13062109684414176253/library_double.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT true --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25T8B8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.988529652891350500.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:23 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:03:23 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B8B25T
INFO 2025-04-24 13:03:23 SortedBasecallsConverter Tile Read Executor - Queueing: 1 TileProcessor jobs
INFO 2025-04-24 13:03:23 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:03:23 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:03:23 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
[Thu Apr 24 13:03:23 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:23 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/dualBarcode.true64111096614849045/library_double.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT true --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25T8B8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.7257275223627574681.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:23 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:03:23 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B8B25T
INFO 2025-04-24 13:03:23 SortedBasecallsConverter Tile Read Executor - Queueing: 1 TileProcessor jobs
INFO 2025-04-24 13:03:23 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:03:23 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:03:24 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
[Thu Apr 24 13:03:24 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:24 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/dualBarcode.false16958122791192438823/library_double.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT false --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25T8B8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.13949442756710499536.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:24 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:03:24 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B8B25T
[Thu Apr 24 13:03:24 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:24 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/dualBarcode.false10802131620843425335/library_double.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT false --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25T8B8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.3729464015818020421.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:24 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:03:24 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B8B25T
[Thu Apr 24 13:03:24 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:24 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/cbclConvert.true152119798047577996/library_double.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT true --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 151T8B8B151T --BASECALLS_DIR testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.10098826884307587554.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:24 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:03:24 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 151T8B8B151T
INFO 2025-04-24 13:03:24 SortedBasecallsConverter Tile Read Executor - Queueing: 2 TileProcessor jobs
INFO 2025-04-24 13:03:26 CbclReader Processing tile 1101
INFO 2025-04-24 13:03:26 CbclReader Processing tile 1102
INFO 2025-04-24 13:03:26 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:03:26 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:03:26 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:03:26 SortedBasecallsConverter Tile 1102 Writer Executor Starting
INFO 2025-04-24 13:03:26 SortedBasecallsConverter Done with awaitExecutor: Tile 1102 Writer Executor
[Thu Apr 24 13:03:26 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:26 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/cbclConvert.true673525518779984902/library_double.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT true --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 151T8B8B151T --BASECALLS_DIR testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.6527880199121710903.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:26 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:03:26 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 151T8B8B151T
INFO 2025-04-24 13:03:26 SortedBasecallsConverter Tile Read Executor - Queueing: 2 TileProcessor jobs
INFO 2025-04-24 13:03:28 CbclReader Processing tile 1102
INFO 2025-04-24 13:03:28 CbclReader Processing tile 1101
INFO 2025-04-24 13:03:28 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:03:28 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:03:28 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:03:28 SortedBasecallsConverter Tile 1102 Writer Executor Starting
INFO 2025-04-24 13:03:28 SortedBasecallsConverter Done with awaitExecutor: Tile 1102 Writer Executor
[Thu Apr 24 13:03:28 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:28 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/cbclConvert.false8303623054940142952/library_double.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT false --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 151T8B8B151T --BASECALLS_DIR testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.11665140390195980124.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:28 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:03:28 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 151T8B8B151T
INFO 2025-04-24 13:03:28 CbclReader Processing tile 1101
INFO 2025-04-24 13:03:29 CbclReader Processing tile 1102
[Thu Apr 24 13:03:29 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1487929344
[Thu Apr 24 13:03:29 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/cbclConvert.false17529057895023287636/library_double.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT false --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 151T8B8B151T --BASECALLS_DIR testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.15982774065531243023.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:29 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:03:29 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 151T8B8B151T
INFO 2025-04-24 13:03:29 CbclReader Processing tile 1101
INFO 2025-04-24 13:03:29 CbclReader Processing tile 1102
[Thu Apr 24 13:03:29 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1487929344
[Thu Apr 24 13:03:29 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/hiseqxSingleLocs.true11766598724575373953/library_double.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT true --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25T8B8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.17023533672670765952.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:29 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:03:29 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B8B25T
INFO 2025-04-24 13:03:29 SortedBasecallsConverter Tile Read Executor - Queueing: 2 TileProcessor jobs
INFO 2025-04-24 13:03:29 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:03:29 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:03:30 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:03:30 SortedBasecallsConverter Tile 1102 Writer Executor Starting
INFO 2025-04-24 13:03:30 SortedBasecallsConverter Done with awaitExecutor: Tile 1102 Writer Executor
[Thu Apr 24 13:03:30 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:30 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/hiseqxSingleLocs.true7773729266856509893/library_double.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT true --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25T8B8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.8713564281391492374.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:30 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:03:30 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B8B25T
INFO 2025-04-24 13:03:30 SortedBasecallsConverter Tile Read Executor - Queueing: 2 TileProcessor jobs
INFO 2025-04-24 13:03:30 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:03:30 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:03:31 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:03:31 SortedBasecallsConverter Tile 1102 Writer Executor Starting
INFO 2025-04-24 13:03:31 SortedBasecallsConverter Done with awaitExecutor: Tile 1102 Writer Executor
[Thu Apr 24 13:03:31 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:31 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/hiseqxSingleLocs.false773130746282886639/library_double.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT false --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25T8B8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.6294954546094161481.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:31 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:03:31 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B8B25T
[Thu Apr 24 13:03:31 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:31 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/hiseqxSingleLocs.false14054468242060168845/library_double.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT false --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25T8B8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.17199940369856015609.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:31 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:03:31 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B8B25T
[Thu Apr 24 13:03:31 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:31 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/hiseqxSingleLocs.true12548543278690393386/library_double.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT true --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25T8B8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.9509736330271184975.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:31 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:03:31 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B8B25T
INFO 2025-04-24 13:03:31 SortedBasecallsConverter Tile Read Executor - Queueing: 2 TileProcessor jobs
INFO 2025-04-24 13:03:31 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:03:31 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:03:32 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:03:32 SortedBasecallsConverter Tile 1102 Writer Executor Starting
INFO 2025-04-24 13:03:32 SortedBasecallsConverter Done with awaitExecutor: Tile 1102 Writer Executor
[Thu Apr 24 13:03:32 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:32 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/hiseqxSingleLocs.true2900875513624308150/library_double.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT true --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25T8B8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.18272203854540276754.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:32 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:03:32 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B8B25T
INFO 2025-04-24 13:03:32 SortedBasecallsConverter Tile Read Executor - Queueing: 2 TileProcessor jobs
INFO 2025-04-24 13:03:32 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:03:32 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:03:33 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:03:33 SortedBasecallsConverter Tile 1102 Writer Executor Starting
INFO 2025-04-24 13:03:33 SortedBasecallsConverter Done with awaitExecutor: Tile 1102 Writer Executor
[Thu Apr 24 13:03:33 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:33 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/hiseqxSingleLocs.false12508701264686851079/library_double.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT false --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25T8B8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.13592732741216735340.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:33 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:03:33 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B8B25T
[Thu Apr 24 13:03:33 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:33 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/hiseqxSingleLocs.false7545145901278813197/library_double.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT false --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25T8B8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.7971557449487054205.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:33 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:03:33 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B8B25T
[Thu Apr 24 13:03:33 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:34 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/dualBarcode.true7497196612340052347/library_double.params --PROCESS_SINGLE_TILE 1101 --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT true --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25T8B8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.15976023660881833951.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:34 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:03:34 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B8B25T
INFO 2025-04-24 13:03:34 SortedBasecallsConverter Tile Read Executor - Queueing: 1 TileProcessor jobs
INFO 2025-04-24 13:03:34 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:03:34 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:03:34 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
[Thu Apr 24 13:03:34 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:34 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/dualBarcode.true10077229288412193926/library_double.params --PROCESS_SINGLE_TILE 1101 --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT true --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25T8B8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.10353192912085531746.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:34 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:03:34 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B8B25T
INFO 2025-04-24 13:03:34 SortedBasecallsConverter Tile Read Executor - Queueing: 1 TileProcessor jobs
INFO 2025-04-24 13:03:34 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:03:34 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:03:34 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
[Thu Apr 24 13:03:34 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:34 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/dualBarcode.false9197425028946906703/library_double.params --PROCESS_SINGLE_TILE 1101 --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT false --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25T8B8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.12369297923586743650.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:34 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:03:35 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B8B25T
[Thu Apr 24 13:03:35 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:35 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/dualBarcode.false17396055121422910033/library_double.params --PROCESS_SINGLE_TILE 1101 --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT false --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25T8B8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.17970137846766579121.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:35 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:03:35 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B8B25T
[Thu Apr 24 13:03:35 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:35 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/multilane.true9423116337684022702/library_double.params --PROCESS_SINGLE_TILE 1101 --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT true --MATCH_BARCODES_INLINE true --LANE 1 --LANE 2 --READ_STRUCTURE 25T8B8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.8492697679621784511.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:35 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:03:35 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B8B25T
INFO 2025-04-24 13:03:35 SortedBasecallsConverter Tile Read Executor - Queueing: 1 TileProcessor jobs
INFO 2025-04-24 13:03:35 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:03:35 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:03:35 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
[Thu Apr 24 13:03:35 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:35 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/multilane.true1903541360648217696/library_double.params --PROCESS_SINGLE_TILE 1101 --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT true --MATCH_BARCODES_INLINE false --LANE 1 --LANE 2 --READ_STRUCTURE 25T8B8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.10238056200547129417.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:35 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:03:35 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B8B25T
INFO 2025-04-24 13:03:35 SortedBasecallsConverter Tile Read Executor - Queueing: 1 TileProcessor jobs
INFO 2025-04-24 13:03:35 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:03:35 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:03:36 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
[Thu Apr 24 13:03:36 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:36 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/multilane.false16744216493163117383/library_double.params --PROCESS_SINGLE_TILE 1101 --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT false --MATCH_BARCODES_INLINE true --LANE 1 --LANE 2 --READ_STRUCTURE 25T8B8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.13471023364819691695.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:36 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:03:36 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B8B25T
[Thu Apr 24 13:03:36 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:36 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/multilane.false16629127160220943548/library_double.params --PROCESS_SINGLE_TILE 1101 --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT false --MATCH_BARCODES_INLINE false --LANE 1 --LANE 2 --READ_STRUCTURE 25T8B8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.8877715442624039177.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:36 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:03:36 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B8B25T
[Thu Apr 24 13:03:36 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:36 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/cbclConvert.true8904400071366669386/library_double.params --PROCESS_SINGLE_TILE 1102 --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT true --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 151T8B8B151T --BASECALLS_DIR testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.11530958112361709890.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:36 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:03:36 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 151T8B8B151T
INFO 2025-04-24 13:03:36 SortedBasecallsConverter Tile Read Executor - Queueing: 1 TileProcessor jobs
INFO 2025-04-24 13:03:36 CbclReader Processing tile 1102
INFO 2025-04-24 13:03:36 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:03:36 SortedBasecallsConverter Tile 1102 Writer Executor Starting
INFO 2025-04-24 13:03:36 SortedBasecallsConverter Done with awaitExecutor: Tile 1102 Writer Executor
[Thu Apr 24 13:03:36 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:36 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/cbclConvert.true15431638112788674519/library_double.params --PROCESS_SINGLE_TILE 1102 --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT true --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 151T8B8B151T --BASECALLS_DIR testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.13558125025901389433.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:36 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:03:36 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 151T8B8B151T
INFO 2025-04-24 13:03:36 SortedBasecallsConverter Tile Read Executor - Queueing: 1 TileProcessor jobs
INFO 2025-04-24 13:03:37 CbclReader Processing tile 1102
INFO 2025-04-24 13:03:37 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:03:37 SortedBasecallsConverter Tile 1102 Writer Executor Starting
INFO 2025-04-24 13:03:37 SortedBasecallsConverter Done with awaitExecutor: Tile 1102 Writer Executor
[Thu Apr 24 13:03:37 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:37 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/cbclConvert.false8120073646914259103/library_double.params --PROCESS_SINGLE_TILE 1102 --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT false --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 151T8B8B151T --BASECALLS_DIR testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.7942550869982376373.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:37 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:03:37 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 151T8B8B151T
INFO 2025-04-24 13:03:37 CbclReader Processing tile 1102
[Thu Apr 24 13:03:37 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:37 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/cbclConvert.false12196082998964678624/library_double.params --PROCESS_SINGLE_TILE 1102 --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT false --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 151T8B8B151T --BASECALLS_DIR testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.15843094069029974346.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:37 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:03:37 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 151T8B8B151T
INFO 2025-04-24 13:03:38 CbclReader Processing tile 1102
[Thu Apr 24 13:03:38 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1503657984
[Thu Apr 24 13:03:38 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/barcodes --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/cbclConvert.true5510104930077199946/library_double.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT true --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 151T8B8B151T --BASECALLS_DIR testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.15285665342464491833.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:38 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:03:38 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 151T8B8B151T
INFO 2025-04-24 13:03:38 SortedBasecallsConverter Tile Read Executor - Queueing: 2 TileProcessor jobs
INFO 2025-04-24 13:03:39 CbclReader Processing tile 1101
INFO 2025-04-24 13:03:39 CbclReader Processing tile 1102
INFO 2025-04-24 13:03:39 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:03:39 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:03:40 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:03:40 SortedBasecallsConverter Tile 1102 Writer Executor Starting
INFO 2025-04-24 13:03:40 SortedBasecallsConverter Done with awaitExecutor: Tile 1102 Writer Executor
[Thu Apr 24 13:03:40 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:40 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/barcodes --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/cbclConvert.true6123071794974614053/library_double.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT true --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 151T8B8B151T --BASECALLS_DIR testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.11532808057994428741.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:40 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:03:40 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 151T8B8B151T
INFO 2025-04-24 13:03:40 SortedBasecallsConverter Tile Read Executor - Queueing: 2 TileProcessor jobs
INFO 2025-04-24 13:03:42 CbclReader Processing tile 1102
INFO 2025-04-24 13:03:42 CbclReader Processing tile 1101
INFO 2025-04-24 13:03:42 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:03:42 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:03:42 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:03:42 SortedBasecallsConverter Tile 1102 Writer Executor Starting
INFO 2025-04-24 13:03:42 SortedBasecallsConverter Done with awaitExecutor: Tile 1102 Writer Executor
[Thu Apr 24 13:03:42 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:42 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/barcodes --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/cbclConvert.false9677185273294366252/library_double.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT false --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 151T8B8B151T --BASECALLS_DIR testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.7347723600121611838.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:42 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:03:42 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 151T8B8B151T
INFO 2025-04-24 13:03:42 CbclReader Processing tile 1101
INFO 2025-04-24 13:03:43 CbclReader Processing tile 1102
[Thu Apr 24 13:03:43 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1503657984
[Thu Apr 24 13:03:43 EDT 2025] IlluminaBasecallsToSam --BARCODES_DIR testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/barcodes --RUN_BARCODE HiMom --SEQUENCING_CENTER BI --INCLUDE_BC_IN_RG_TAG false --LIBRARY_PARAMS /tmp/cbclConvert.false12533021876579687901/library_double.params --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT false --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 151T8B8B151T --BASECALLS_DIR testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.3548865725202059318.metrics --PLATFORM ILLUMINA --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:43 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:03:43 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 151T8B8B151T
INFO 2025-04-24 13:03:43 CbclReader Processing tile 1101
INFO 2025-04-24 13:03:43 CbclReader Processing tile 1102
[Thu Apr 24 13:03:43 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1440743424