Class picard.illumina.IlluminaBasecallsToSamAdapterClippingTest
|
100%
successful |
Tests
| Test | Duration | Result |
|---|---|---|
| testBasic[0](1, 125T125T, null, null, 32) | 0.731s | passed |
| testBasic[10](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32) | 0.560s | passed |
| testBasic[11](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108) | 0.507s | passed |
| testBasic[1](2, 125T125T, null, null, 108) | 0.624s | passed |
| testBasic[2](1, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0) | 0.540s | passed |
| testBasic[3](2, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0) | 0.539s | passed |
| testBasic[4](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0) | 0.605s | passed |
| testBasic[5](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0) | 0.583s | passed |
| testBasic[6](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0) | 0.644s | passed |
| testBasic[7](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0) | 0.521s | passed |
| testBasic[8](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32) | 0.538s | passed |
| testBasic[9](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108) | 0.553s | passed |
Standard error
[Thu Apr 24 13:01:25 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/.1.illuminaBasecallsToSam2446372814731552301.sam --RUN_BARCODE 305PJAAXX080716 --SAMPLE_ALIAS myalias --SEQUENCING_CENTER BI --LANE 1 --READ_STRUCTURE 125T125T --BASECALLS_DIR testdata/picard/illumina/125T125T/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 --SORT true --MATCH_BARCODES_INLINE 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 13:01:25 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 13:01:25 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 125T125T INFO 2025-04-24 13:01:25 SortedBasecallsConverter Tile Read Executor - Queueing: 1 TileProcessor jobs INFO 2025-04-24 13:01:26 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor INFO 2025-04-24 13:01:26 SortedBasecallsConverter Tile 1101 Writer Executor Starting INFO 2025-04-24 13:01:26 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor [Thu Apr 24 13:01:26 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:01:26 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/.2.illuminaBasecallsToSam8686600400704208947.sam --RUN_BARCODE 305PJAAXX080716 --SAMPLE_ALIAS myalias --SEQUENCING_CENTER BI --LANE 2 --READ_STRUCTURE 125T125T --BASECALLS_DIR testdata/picard/illumina/125T125T/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 --SORT true --MATCH_BARCODES_INLINE 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 13:01:26 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 13:01:26 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 125T125T INFO 2025-04-24 13:01:26 SortedBasecallsConverter Tile Read Executor - Queueing: 1 TileProcessor jobs INFO 2025-04-24 13:01:26 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor INFO 2025-04-24 13:01:26 SortedBasecallsConverter Tile 1101 Writer Executor Starting INFO 2025-04-24 13:01:26 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor [Thu Apr 24 13:01:26 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:01:27 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/.1.illuminaBasecallsToSam13191586707105207123.sam --RUN_BARCODE 305PJAAXX080716 --SAMPLE_ALIAS myalias --SEQUENCING_CENTER BI --FIVE_PRIME_ADAPTER ACGTACGTACGTACGT --THREE_PRIME_ADAPTER ACGTACGTACGTACGT --LANE 1 --READ_STRUCTURE 125T125T --BASECALLS_DIR testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls --PLATFORM ILLUMINA --INCLUDE_BC_IN_RG_TAG false --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 --SORT true --MATCH_BARCODES_INLINE 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 13:01:27 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 13:01:27 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 125T125T INFO 2025-04-24 13:01:27 SortedBasecallsConverter Tile Read Executor - Queueing: 1 TileProcessor jobs INFO 2025-04-24 13:01:27 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor INFO 2025-04-24 13:01:27 SortedBasecallsConverter Tile 1101 Writer Executor Starting INFO 2025-04-24 13:01:27 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor [Thu Apr 24 13:01:27 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:01:27 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/.2.illuminaBasecallsToSam1613113885656668656.sam --RUN_BARCODE 305PJAAXX080716 --SAMPLE_ALIAS myalias --SEQUENCING_CENTER BI --FIVE_PRIME_ADAPTER ACGTACGTACGTACGT --THREE_PRIME_ADAPTER ACGTACGTACGTACGT --LANE 2 --READ_STRUCTURE 125T125T --BASECALLS_DIR testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls --PLATFORM ILLUMINA --INCLUDE_BC_IN_RG_TAG false --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 --SORT true --MATCH_BARCODES_INLINE 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 13:01:27 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 13:01:27 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 125T125T INFO 2025-04-24 13:01:27 SortedBasecallsConverter Tile Read Executor - Queueing: 1 TileProcessor jobs INFO 2025-04-24 13:01:27 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor INFO 2025-04-24 13:01:27 SortedBasecallsConverter Tile 1101 Writer Executor Starting INFO 2025-04-24 13:01:28 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor [Thu Apr 24 13:01:28 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1503657984 [Thu Apr 24 13:01:28 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/.1.illuminaBasecallsToSam9984318794136007790.sam --RUN_BARCODE 305PJAAXX080716 --SAMPLE_ALIAS myalias --SEQUENCING_CENTER BI --FIVE_PRIME_ADAPTER AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG --THREE_PRIME_ADAPTER CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG --LANE 1 --READ_STRUCTURE 125T125T --BASECALLS_DIR testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls --PLATFORM ILLUMINA --INCLUDE_BC_IN_RG_TAG false --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 --SORT true --MATCH_BARCODES_INLINE 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 13:01:28 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 13:01:28 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 125T125T INFO 2025-04-24 13:01:28 SortedBasecallsConverter Tile Read Executor - Queueing: 1 TileProcessor jobs INFO 2025-04-24 13:01:28 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor INFO 2025-04-24 13:01:28 SortedBasecallsConverter Tile 1101 Writer Executor Starting INFO 2025-04-24 13:01:28 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor [Thu Apr 24 13:01:28 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:01:28 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/.2.illuminaBasecallsToSam8784481760768917188.sam --RUN_BARCODE 305PJAAXX080716 --SAMPLE_ALIAS myalias --SEQUENCING_CENTER BI --FIVE_PRIME_ADAPTER AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG --THREE_PRIME_ADAPTER CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG --LANE 2 --READ_STRUCTURE 125T125T --BASECALLS_DIR testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls --PLATFORM ILLUMINA --INCLUDE_BC_IN_RG_TAG false --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 --SORT true --MATCH_BARCODES_INLINE 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 13:01:28 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 13:01:28 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 125T125T INFO 2025-04-24 13:01:28 SortedBasecallsConverter Tile Read Executor - Queueing: 1 TileProcessor jobs INFO 2025-04-24 13:01:28 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor INFO 2025-04-24 13:01:28 SortedBasecallsConverter Tile 1101 Writer Executor Starting INFO 2025-04-24 13:01:29 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor [Thu Apr 24 13:01:29 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:01:29 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/.1.illuminaBasecallsToSam15664644237092176707.sam --RUN_BARCODE 305PJAAXX080716 --SAMPLE_ALIAS myalias --SEQUENCING_CENTER BI --FIVE_PRIME_ADAPTER AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA --THREE_PRIME_ADAPTER AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG --LANE 1 --READ_STRUCTURE 125T125T --BASECALLS_DIR testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls --PLATFORM ILLUMINA --INCLUDE_BC_IN_RG_TAG false --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 --SORT true --MATCH_BARCODES_INLINE 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 13:01:29 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 13:01:29 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 125T125T INFO 2025-04-24 13:01:29 SortedBasecallsConverter Tile Read Executor - Queueing: 1 TileProcessor jobs INFO 2025-04-24 13:01:29 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor INFO 2025-04-24 13:01:29 SortedBasecallsConverter Tile 1101 Writer Executor Starting INFO 2025-04-24 13:01:29 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor [Thu Apr 24 13:01:29 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:01:29 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/.2.illuminaBasecallsToSam6718632372792563242.sam --RUN_BARCODE 305PJAAXX080716 --SAMPLE_ALIAS myalias --SEQUENCING_CENTER BI --FIVE_PRIME_ADAPTER AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA --THREE_PRIME_ADAPTER AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG --LANE 2 --READ_STRUCTURE 125T125T --BASECALLS_DIR testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls --PLATFORM ILLUMINA --INCLUDE_BC_IN_RG_TAG false --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 --SORT true --MATCH_BARCODES_INLINE 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 13:01:29 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 13:01:29 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 125T125T INFO 2025-04-24 13:01:29 SortedBasecallsConverter Tile Read Executor - Queueing: 1 TileProcessor jobs INFO 2025-04-24 13:01:30 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor INFO 2025-04-24 13:01:30 SortedBasecallsConverter Tile 1101 Writer Executor Starting INFO 2025-04-24 13:01:30 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor [Thu Apr 24 13:01:30 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:01:30 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/.1.illuminaBasecallsToSam3451831827655201599.sam --RUN_BARCODE 305PJAAXX080716 --SAMPLE_ALIAS myalias --SEQUENCING_CENTER BI --FIVE_PRIME_ADAPTER AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT --THREE_PRIME_ADAPTER AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG --LANE 1 --READ_STRUCTURE 125T125T --BASECALLS_DIR testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls --PLATFORM ILLUMINA --INCLUDE_BC_IN_RG_TAG false --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 --SORT true --MATCH_BARCODES_INLINE 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 13:01:30 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 13:01:30 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 125T125T INFO 2025-04-24 13:01:30 SortedBasecallsConverter Tile Read Executor - Queueing: 1 TileProcessor jobs INFO 2025-04-24 13:01:30 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor INFO 2025-04-24 13:01:30 SortedBasecallsConverter Tile 1101 Writer Executor Starting INFO 2025-04-24 13:01:30 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor [Thu Apr 24 13:01:30 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:01:30 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/.2.illuminaBasecallsToSam9172370487992420866.sam --RUN_BARCODE 305PJAAXX080716 --SAMPLE_ALIAS myalias --SEQUENCING_CENTER BI --FIVE_PRIME_ADAPTER AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT --THREE_PRIME_ADAPTER AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG --LANE 2 --READ_STRUCTURE 125T125T --BASECALLS_DIR testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls --PLATFORM ILLUMINA --INCLUDE_BC_IN_RG_TAG false --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 --SORT true --MATCH_BARCODES_INLINE 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 13:01:30 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 13:01:31 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 125T125T INFO 2025-04-24 13:01:31 SortedBasecallsConverter Tile Read Executor - Queueing: 1 TileProcessor jobs INFO 2025-04-24 13:01:31 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor INFO 2025-04-24 13:01:31 SortedBasecallsConverter Tile 1101 Writer Executor Starting INFO 2025-04-24 13:01:31 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor [Thu Apr 24 13:01:31 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:01:31 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/.1.illuminaBasecallsToSam11997308563938595857.sam --RUN_BARCODE 305PJAAXX080716 --SAMPLE_ALIAS myalias --SEQUENCING_CENTER BI --FIVE_PRIME_ADAPTER AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --THREE_PRIME_ADAPTER AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG --LANE 1 --READ_STRUCTURE 125T125T --BASECALLS_DIR testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls --PLATFORM ILLUMINA --INCLUDE_BC_IN_RG_TAG false --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 --SORT true --MATCH_BARCODES_INLINE 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 13:01:31 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 13:01:31 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 125T125T INFO 2025-04-24 13:01:31 SortedBasecallsConverter Tile Read Executor - Queueing: 1 TileProcessor jobs INFO 2025-04-24 13:01:31 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor INFO 2025-04-24 13:01:31 SortedBasecallsConverter Tile 1101 Writer Executor Starting INFO 2025-04-24 13:01:32 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor [Thu Apr 24 13:01:32 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:01:32 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/.2.illuminaBasecallsToSam11401690021603448336.sam --RUN_BARCODE 305PJAAXX080716 --SAMPLE_ALIAS myalias --SEQUENCING_CENTER BI --FIVE_PRIME_ADAPTER AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --THREE_PRIME_ADAPTER AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG --LANE 2 --READ_STRUCTURE 125T125T --BASECALLS_DIR testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls --PLATFORM ILLUMINA --INCLUDE_BC_IN_RG_TAG false --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 --SORT true --MATCH_BARCODES_INLINE 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 125T125T INFO 2025-04-24 13:01:32 SortedBasecallsConverter Tile Read Executor - Queueing: 1 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 [Thu Apr 24 13:01:32 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824