Class picard.illumina.IlluminaBasecallsToFastqTest
Tests
| Test |
Duration |
Result |
| testAdapterTrimming |
0.416s |
passed |
| testCbclConvert |
6.902s |
passed |
| testCustomAdapterTrimming |
0.380s |
passed |
| testDeMultiplexed |
10.745s |
passed |
| testDeMultiplexedWithIndex |
11.169s |
passed |
| testDeMultiplexedWithtwoIndexes |
11.121s |
passed |
| testDualBarcodes |
1.364s |
passed |
| testHiseqxSingleLocs |
2.333s |
passed |
| testMultipleLanes |
2.325s |
passed |
| testMultiplexWithIlluminaReadNameHeaders |
0.358s |
passed |
| testNonBarcoded |
0.417s |
passed |
| testQualityAndAdapterTrimming |
0.415s |
passed |
| testQualityTrimming |
0.417s |
passed |
Standard error
[Thu Apr 24 13:00:37 EDT 2025] IlluminaBasecallsToFastq --OUTPUT_PREFIX /tmp/adapterTrimmed.15540680178868862515 --RUN_BARCODE HiMom --MACHINE_NAME machine1 --FLOWCELL_BARCODE abcdeACXX --ADAPTERS_TO_CHECK PAIRED_END --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK SINGLE_END --ADAPTERS_TO_CHECK NEXTERA_V1 --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK FLUIDIGM --ADAPTERS_TO_CHECK TRUSEQ_SMALLRNA --ADAPTERS_TO_CHECK ALTERNATIVE_SINGLE_END --LANE 1 --READ_STRUCTURE 25T8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --MAX_RECORDS_IN_RAM 100 --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --FORCE_GC true --SORT true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --READ_NAME_FORMAT CASAVA_1_8 --MATCH_BARCODES_INLINE false --MIN_TRIMMED_LENGTH 20 --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 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:37 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 13:00:37 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B25T
INFO 2025-04-24 13:00:37 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:00:37 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:00:37 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:00:37 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:00:37 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:00:37 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:00:37 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:00:37 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:00:37 EDT 2025] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:37 EDT 2025] IlluminaBasecallsToFastq --RUN_BARCODE HiMom --MACHINE_NAME machine1 --FLOWCELL_BARCODE abcdeACXX --MULTIPLEX_PARAMS /tmp/dualBarcode..dir2766994890989699976/barcode_double.params --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.12147024846029273138.metrics --MAX_RECORDS_IN_RAM 1000 --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --FORCE_GC true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --READ_NAME_FORMAT CASAVA_1_8 --MIN_TRIMMED_LENGTH 20 --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 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:37 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 13:00:37 IlluminaBasecallsToFastq READ STRUCTURE IS 151T8B8B151T
INFO 2025-04-24 13:00:37 SortedBasecallsConverter Tile Read Executor - Queueing: 2 TileProcessor jobs
INFO 2025-04-24 13:00:40 CbclReader Processing tile 1101
INFO 2025-04-24 13:00:40 CbclReader Processing tile 1102
INFO 2025-04-24 13:00:40 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:00:40 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:00:40 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:00:40 SortedBasecallsConverter Tile 1102 Writer Executor Starting
INFO 2025-04-24 13:00:40 SortedBasecallsConverter Done with awaitExecutor: Tile 1102 Writer Executor
[Thu Apr 24 13:00:40 EDT 2025] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:40 EDT 2025] IlluminaBasecallsToFastq --RUN_BARCODE HiMom --MACHINE_NAME machine1 --FLOWCELL_BARCODE abcdeACXX --MULTIPLEX_PARAMS /tmp/dualBarcode..dir2766994890989699976/barcode_double.params --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.17588924806976587514.metrics --MAX_RECORDS_IN_RAM 1000 --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --FORCE_GC true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --READ_NAME_FORMAT CASAVA_1_8 --MIN_TRIMMED_LENGTH 20 --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 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:40 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 13:00:40 IlluminaBasecallsToFastq READ STRUCTURE IS 151T8B8B151T
INFO 2025-04-24 13:00:40 SortedBasecallsConverter Tile Read Executor - Queueing: 2 TileProcessor jobs
INFO 2025-04-24 13:00:42 CbclReader Processing tile 1101
INFO 2025-04-24 13:00:42 CbclReader Processing tile 1102
INFO 2025-04-24 13:00:42 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:00:42 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:00:42 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:00:42 SortedBasecallsConverter Tile 1102 Writer Executor Starting
INFO 2025-04-24 13:00:43 SortedBasecallsConverter Done with awaitExecutor: Tile 1102 Writer Executor
[Thu Apr 24 13:00:43 EDT 2025] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:43 EDT 2025] IlluminaBasecallsToFastq --RUN_BARCODE HiMom --MACHINE_NAME machine1 --FLOWCELL_BARCODE abcdeACXX --MULTIPLEX_PARAMS /tmp/dualBarcode..dir2766994890989699976/barcode_double.params --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.12613681691654682698.metrics --MAX_RECORDS_IN_RAM 1000 --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --FORCE_GC true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --READ_NAME_FORMAT CASAVA_1_8 --MIN_TRIMMED_LENGTH 20 --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 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:43 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 13:00:43 IlluminaBasecallsToFastq READ STRUCTURE IS 151T8B8B151T
INFO 2025-04-24 13:00:43 CbclReader Processing tile 1101
INFO 2025-04-24 13:00:43 CbclReader Processing tile 1102
[Thu Apr 24 13:00:43 EDT 2025] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:43 EDT 2025] IlluminaBasecallsToFastq --RUN_BARCODE HiMom --MACHINE_NAME machine1 --FLOWCELL_BARCODE abcdeACXX --MULTIPLEX_PARAMS /tmp/dualBarcode..dir2766994890989699976/barcode_double.params --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.52774683831221455.metrics --MAX_RECORDS_IN_RAM 1000 --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --FORCE_GC true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --READ_NAME_FORMAT CASAVA_1_8 --MIN_TRIMMED_LENGTH 20 --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 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:43 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 13:00:43 IlluminaBasecallsToFastq READ STRUCTURE IS 151T8B8B151T
INFO 2025-04-24 13:00:44 CbclReader Processing tile 1101
INFO 2025-04-24 13:00:44 CbclReader Processing tile 1102
[Thu Apr 24 13:00:44 EDT 2025] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1503657984
[Thu Apr 24 13:00:44 EDT 2025] IlluminaBasecallsToFastq --OUTPUT_PREFIX /tmp/adapterTrimmed.7772737820521190881 --RUN_BARCODE HiMom --MACHINE_NAME machine1 --FLOWCELL_BARCODE abcdeACXX --FIVE_PRIME_ADAPTER CGGCC --THREE_PRIME_ADAPTER TGGGC --LANE 1 --READ_STRUCTURE 25T8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --MAX_RECORDS_IN_RAM 100 --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --FORCE_GC true --SORT true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --READ_NAME_FORMAT CASAVA_1_8 --MATCH_BARCODES_INLINE false --MIN_TRIMMED_LENGTH 20 --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 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:44 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 13:00:44 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B25T
INFO 2025-04-24 13:00:44 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:00:44 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:00:44 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:00:44 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:00:44 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:00:44 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:00:44 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:00:44 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:00:44 EDT 2025] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:45 EDT 2025] IlluminaBasecallsToFastq --RUN_BARCODE HiMom --MACHINE_NAME machine1 --FLOWCELL_BARCODE abcdeACXX --MULTIPLEX_PARAMS /tmp/multiplexedBarcode..dir17484135972369367518/mp_barcode.params --SORT true --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25T8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.8117739262356622547.metrics --MAX_RECORDS_IN_RAM 1000 --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --FORCE_GC true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --READ_NAME_FORMAT CASAVA_1_8 --MIN_TRIMMED_LENGTH 20 --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 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:45 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 13:00:45 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B25T
INFO 2025-04-24 13:00:45 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:00:45 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:00:45 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:00:46 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:00:46 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:00:48 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:00:48 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:00:50 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:00:50 EDT 2025] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:50 EDT 2025] IlluminaBasecallsToFastq --RUN_BARCODE HiMom --MACHINE_NAME machine1 --FLOWCELL_BARCODE abcdeACXX --MULTIPLEX_PARAMS /tmp/multiplexedBarcode..dir17484135972369367518/mp_barcode.params --SORT true --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25T8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.1189289103062096656.metrics --MAX_RECORDS_IN_RAM 1000 --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --FORCE_GC true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --READ_NAME_FORMAT CASAVA_1_8 --MIN_TRIMMED_LENGTH 20 --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 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:50 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 13:00:50 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B25T
INFO 2025-04-24 13:00:50 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:00:50 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:00:50 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:00:51 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:00:51 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:00:53 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:00:53 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:00:55 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:00:55 EDT 2025] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:55 EDT 2025] IlluminaBasecallsToFastq --RUN_BARCODE HiMom --MACHINE_NAME machine1 --FLOWCELL_BARCODE abcdeACXX --MULTIPLEX_PARAMS /tmp/multiplexedBarcode..dir17484135972369367518/mp_barcode.params --SORT false --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25T8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.18442558315697345959.metrics --MAX_RECORDS_IN_RAM 1000 --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --FORCE_GC true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --READ_NAME_FORMAT CASAVA_1_8 --MIN_TRIMMED_LENGTH 20 --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 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:55 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 13:00:55 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B25T
[Thu Apr 24 13:00:55 EDT 2025] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:55 EDT 2025] IlluminaBasecallsToFastq --RUN_BARCODE HiMom --MACHINE_NAME machine1 --FLOWCELL_BARCODE abcdeACXX --MULTIPLEX_PARAMS /tmp/multiplexedBarcode..dir17484135972369367518/mp_barcode.params --SORT false --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25T8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.4640701071974801566.metrics --MAX_RECORDS_IN_RAM 1000 --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --FORCE_GC true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --READ_NAME_FORMAT CASAVA_1_8 --MIN_TRIMMED_LENGTH 20 --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 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:55 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 13:00:55 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B25T
[Thu Apr 24 13:00:55 EDT 2025] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:55 EDT 2025] IlluminaBasecallsToFastq --RUN_BARCODE HiMom --MACHINE_NAME machine1 --FLOWCELL_BARCODE abcdeACXX --MULTIPLEX_PARAMS /tmp/multiplexedBarcodeWithIndex..dir10811797242773407425/mp_barcode.params --SORT true --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25T8B4M21T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.13241389032458088167.metrics --MAX_RECORDS_IN_RAM 1000 --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --FORCE_GC true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --READ_NAME_FORMAT CASAVA_1_8 --MIN_TRIMMED_LENGTH 20 --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 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:55 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 13:00:55 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B4M21T
INFO 2025-04-24 13:00:55 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:00:55 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:00:55 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:00:57 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:00:57 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:00:59 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:00:59 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:01:00 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:01:00 EDT 2025] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:01 EDT 2025] IlluminaBasecallsToFastq --RUN_BARCODE HiMom --MACHINE_NAME machine1 --FLOWCELL_BARCODE abcdeACXX --MULTIPLEX_PARAMS /tmp/multiplexedBarcodeWithIndex..dir10811797242773407425/mp_barcode.params --SORT true --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25T8B4M21T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.14602170846810019186.metrics --MAX_RECORDS_IN_RAM 1000 --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --FORCE_GC true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --READ_NAME_FORMAT CASAVA_1_8 --MIN_TRIMMED_LENGTH 20 --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 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:01 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 13:01:01 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B4M21T
INFO 2025-04-24 13:01:01 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:01:01 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:01:01 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:01:02 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:01:02 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:01:04 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:01:04 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:01:06 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:01:06 EDT 2025] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:06 EDT 2025] IlluminaBasecallsToFastq --RUN_BARCODE HiMom --MACHINE_NAME machine1 --FLOWCELL_BARCODE abcdeACXX --MULTIPLEX_PARAMS /tmp/multiplexedBarcodeWithIndex..dir10811797242773407425/mp_barcode.params --SORT false --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25T8B4M21T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.5877615345568430724.metrics --MAX_RECORDS_IN_RAM 1000 --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --FORCE_GC true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --READ_NAME_FORMAT CASAVA_1_8 --MIN_TRIMMED_LENGTH 20 --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 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:06 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 13:01:06 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B4M21T
[Thu Apr 24 13:01:06 EDT 2025] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:06 EDT 2025] IlluminaBasecallsToFastq --RUN_BARCODE HiMom --MACHINE_NAME machine1 --FLOWCELL_BARCODE abcdeACXX --MULTIPLEX_PARAMS /tmp/multiplexedBarcodeWithIndex..dir10811797242773407425/mp_barcode.params --SORT false --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25T8B4M21T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.14536521433862245442.metrics --MAX_RECORDS_IN_RAM 1000 --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --FORCE_GC true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --READ_NAME_FORMAT CASAVA_1_8 --MIN_TRIMMED_LENGTH 20 --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 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:06 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 13:01:06 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B4M21T
[Thu Apr 24 13:01:06 EDT 2025] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:06 EDT 2025] IlluminaBasecallsToFastq --RUN_BARCODE HiMom --MACHINE_NAME machine1 --FLOWCELL_BARCODE abcdeACXX --MULTIPLEX_PARAMS /tmp/multiplexedBarcodeWithTwoIndexes..dir548478332479042997/mp_barcode.params --SORT true --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25T8B4M4M17T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.8613469589101000762.metrics --MAX_RECORDS_IN_RAM 1000 --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --FORCE_GC true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --READ_NAME_FORMAT CASAVA_1_8 --MIN_TRIMMED_LENGTH 20 --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 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:06 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 13:01:06 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B4M4M17T
INFO 2025-04-24 13:01:06 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:01:06 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:01:06 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:01:08 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:01:08 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:01:10 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:01:10 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:01:12 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:01:12 EDT 2025] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:12 EDT 2025] IlluminaBasecallsToFastq --RUN_BARCODE HiMom --MACHINE_NAME machine1 --FLOWCELL_BARCODE abcdeACXX --MULTIPLEX_PARAMS /tmp/multiplexedBarcodeWithTwoIndexes..dir548478332479042997/mp_barcode.params --SORT true --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25T8B4M4M17T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.15779114640415058402.metrics --MAX_RECORDS_IN_RAM 1000 --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --FORCE_GC true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --READ_NAME_FORMAT CASAVA_1_8 --MIN_TRIMMED_LENGTH 20 --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 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:12 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 13:01:12 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B4M4M17T
INFO 2025-04-24 13:01:12 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:01:12 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:01:12 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:01:14 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:01:14 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:01:15 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:01:15 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:01:17 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:01:17 EDT 2025] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:17 EDT 2025] IlluminaBasecallsToFastq --RUN_BARCODE HiMom --MACHINE_NAME machine1 --FLOWCELL_BARCODE abcdeACXX --MULTIPLEX_PARAMS /tmp/multiplexedBarcodeWithTwoIndexes..dir548478332479042997/mp_barcode.params --SORT false --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25T8B4M4M17T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.4844474303561825029.metrics --MAX_RECORDS_IN_RAM 1000 --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --FORCE_GC true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --READ_NAME_FORMAT CASAVA_1_8 --MIN_TRIMMED_LENGTH 20 --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 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:17 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 13:01:17 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B4M4M17T
[Thu Apr 24 13:01:17 EDT 2025] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:17 EDT 2025] IlluminaBasecallsToFastq --RUN_BARCODE HiMom --MACHINE_NAME machine1 --FLOWCELL_BARCODE abcdeACXX --MULTIPLEX_PARAMS /tmp/multiplexedBarcodeWithTwoIndexes..dir548478332479042997/mp_barcode.params --SORT false --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25T8B4M4M17T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.13355948454956181906.metrics --MAX_RECORDS_IN_RAM 1000 --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --FORCE_GC true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --READ_NAME_FORMAT CASAVA_1_8 --MIN_TRIMMED_LENGTH 20 --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 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:17 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 13:01:17 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B4M4M17T
[Thu Apr 24 13:01:17 EDT 2025] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:18 EDT 2025] IlluminaBasecallsToFastq --RUN_BARCODE HiMom --MACHINE_NAME machine1 --FLOWCELL_BARCODE abcdeACXX --MULTIPLEX_PARAMS /tmp/dualBarcode..dir6676442524084775096/barcode_double.params --SORT true --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25T8B8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.6968240749587991294.metrics --MAX_RECORDS_IN_RAM 1000 --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --FORCE_GC true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --READ_NAME_FORMAT CASAVA_1_8 --MIN_TRIMMED_LENGTH 20 --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 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:18 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 13:01:18 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B8B25T
INFO 2025-04-24 13:01:18 SortedBasecallsConverter Tile Read Executor - Queueing: 1 TileProcessor jobs
INFO 2025-04-24 13:01:18 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:01:18 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:01:18 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
[Thu Apr 24 13:01:18 EDT 2025] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:18 EDT 2025] IlluminaBasecallsToFastq --RUN_BARCODE HiMom --MACHINE_NAME machine1 --FLOWCELL_BARCODE abcdeACXX --MULTIPLEX_PARAMS /tmp/dualBarcode..dir6676442524084775096/barcode_double.params --SORT true --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25T8B8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.285664703933226422.metrics --MAX_RECORDS_IN_RAM 1000 --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --FORCE_GC true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --READ_NAME_FORMAT CASAVA_1_8 --MIN_TRIMMED_LENGTH 20 --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 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:18 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 13:01:18 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B8B25T
INFO 2025-04-24 13:01:18 SortedBasecallsConverter Tile Read Executor - Queueing: 1 TileProcessor jobs
INFO 2025-04-24 13:01:18 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:01:18 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:01:19 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
[Thu Apr 24 13:01:19 EDT 2025] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:19 EDT 2025] IlluminaBasecallsToFastq --RUN_BARCODE HiMom --MACHINE_NAME machine1 --FLOWCELL_BARCODE abcdeACXX --MULTIPLEX_PARAMS /tmp/dualBarcode..dir6676442524084775096/barcode_double.params --SORT false --MATCH_BARCODES_INLINE false --LANE 1 --READ_STRUCTURE 25T8B8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.10933360040724966122.metrics --MAX_RECORDS_IN_RAM 1000 --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --FORCE_GC true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --READ_NAME_FORMAT CASAVA_1_8 --MIN_TRIMMED_LENGTH 20 --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 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:19 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 13:01:19 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B8B25T
[Thu Apr 24 13:01:19 EDT 2025] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1247805440
[Thu Apr 24 13:01:19 EDT 2025] IlluminaBasecallsToFastq --RUN_BARCODE HiMom --MACHINE_NAME machine1 --FLOWCELL_BARCODE abcdeACXX --MULTIPLEX_PARAMS /tmp/dualBarcode..dir6676442524084775096/barcode_double.params --SORT false --MATCH_BARCODES_INLINE true --LANE 1 --READ_STRUCTURE 25T8B8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls --METRICS_FILE /tmp/ibtf.5321933286454422337.metrics --MAX_RECORDS_IN_RAM 1000 --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --FORCE_GC true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --READ_NAME_FORMAT CASAVA_1_8 --MIN_TRIMMED_LENGTH 20 --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 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:19 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 13:01:19 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B8B25T
[Thu Apr 24 13:01:19 EDT 2025] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1247805440
[Thu Apr 24 13:01:19 EDT 2025] IlluminaBasecallsToFastq --RUN_BARCODE HiMom --MACHINE_NAME machine1 --FLOWCELL_BARCODE abcdeACXX --MULTIPLEX_PARAMS /tmp/hiseqxSingleLocs..dir10126612805237222598/barcode_double.params --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.6534037037188187129.metrics --MAX_RECORDS_IN_RAM 1000 --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --FORCE_GC true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --READ_NAME_FORMAT CASAVA_1_8 --MIN_TRIMMED_LENGTH 20 --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 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:19 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 13:01:19 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B8B25T
INFO 2025-04-24 13:01:19 SortedBasecallsConverter Tile Read Executor - Queueing: 2 TileProcessor jobs
INFO 2025-04-24 13:01:19 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:01:19 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:01:19 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:01:19 SortedBasecallsConverter Tile 1102 Writer Executor Starting
INFO 2025-04-24 13:01:20 SortedBasecallsConverter Done with awaitExecutor: Tile 1102 Writer Executor
[Thu Apr 24 13:01:20 EDT 2025] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:20 EDT 2025] IlluminaBasecallsToFastq --RUN_BARCODE HiMom --MACHINE_NAME machine1 --FLOWCELL_BARCODE abcdeACXX --MULTIPLEX_PARAMS /tmp/hiseqxSingleLocs..dir10126612805237222598/barcode_double.params --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.2787407654566379700.metrics --MAX_RECORDS_IN_RAM 1000 --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --FORCE_GC true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --READ_NAME_FORMAT CASAVA_1_8 --MIN_TRIMMED_LENGTH 20 --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 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:20 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 13:01:20 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B8B25T
INFO 2025-04-24 13:01:20 SortedBasecallsConverter Tile Read Executor - Queueing: 2 TileProcessor jobs
INFO 2025-04-24 13:01:20 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:01:20 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:01:20 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:01:20 SortedBasecallsConverter Tile 1102 Writer Executor Starting
INFO 2025-04-24 13:01:21 SortedBasecallsConverter Done with awaitExecutor: Tile 1102 Writer Executor
[Thu Apr 24 13:01:21 EDT 2025] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:21 EDT 2025] IlluminaBasecallsToFastq --RUN_BARCODE HiMom --MACHINE_NAME machine1 --FLOWCELL_BARCODE abcdeACXX --MULTIPLEX_PARAMS /tmp/hiseqxSingleLocs..dir10126612805237222598/barcode_double.params --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.16115356999897981060.metrics --MAX_RECORDS_IN_RAM 1000 --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --FORCE_GC true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --READ_NAME_FORMAT CASAVA_1_8 --MIN_TRIMMED_LENGTH 20 --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 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:21 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 13:01:21 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B8B25T
[Thu Apr 24 13:01:21 EDT 2025] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1077936128
[Thu Apr 24 13:01:21 EDT 2025] IlluminaBasecallsToFastq --RUN_BARCODE HiMom --MACHINE_NAME machine1 --FLOWCELL_BARCODE abcdeACXX --MULTIPLEX_PARAMS /tmp/hiseqxSingleLocs..dir10126612805237222598/barcode_double.params --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.2628988005591062117.metrics --MAX_RECORDS_IN_RAM 1000 --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --FORCE_GC true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --READ_NAME_FORMAT CASAVA_1_8 --MIN_TRIMMED_LENGTH 20 --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 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:21 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 13:01:21 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B8B25T
[Thu Apr 24 13:01:21 EDT 2025] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1077936128
[Thu Apr 24 13:01:21 EDT 2025] IlluminaBasecallsToFastq --RUN_BARCODE HiMom --MACHINE_NAME machine1 --FLOWCELL_BARCODE abcdeACXX --MULTIPLEX_PARAMS /tmp/dualBarcode..dir2176444274401606870/barcode_double.params --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.15718334605434741743.metrics --MAX_RECORDS_IN_RAM 1000 --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --FORCE_GC true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --READ_NAME_FORMAT CASAVA_1_8 --MIN_TRIMMED_LENGTH 20 --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 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:21 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 13:01:21 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B8B25T
INFO 2025-04-24 13:01:21 SortedBasecallsConverter Tile Read Executor - Queueing: 2 TileProcessor jobs
INFO 2025-04-24 13:01:21 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:01:21 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:01:22 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:01:22 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:01:22 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
[Thu Apr 24 13:01:22 EDT 2025] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:22 EDT 2025] IlluminaBasecallsToFastq --RUN_BARCODE HiMom --MACHINE_NAME machine1 --FLOWCELL_BARCODE abcdeACXX --MULTIPLEX_PARAMS /tmp/dualBarcode..dir2176444274401606870/barcode_double.params --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.6370956188030946856.metrics --MAX_RECORDS_IN_RAM 1000 --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --FORCE_GC true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --READ_NAME_FORMAT CASAVA_1_8 --MIN_TRIMMED_LENGTH 20 --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 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:22 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 13:01:22 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B8B25T
INFO 2025-04-24 13:01:22 SortedBasecallsConverter Tile Read Executor - Queueing: 2 TileProcessor jobs
INFO 2025-04-24 13:01:22 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:01:22 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:01:23 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:01:23 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:01:23 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
[Thu Apr 24 13:01:23 EDT 2025] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:23 EDT 2025] IlluminaBasecallsToFastq --RUN_BARCODE HiMom --MACHINE_NAME machine1 --FLOWCELL_BARCODE abcdeACXX --MULTIPLEX_PARAMS /tmp/dualBarcode..dir2176444274401606870/barcode_double.params --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.17346744475582661704.metrics --MAX_RECORDS_IN_RAM 1000 --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --FORCE_GC true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --READ_NAME_FORMAT CASAVA_1_8 --MIN_TRIMMED_LENGTH 20 --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 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:23 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 13:01:23 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B8B25T
[Thu Apr 24 13:01:23 EDT 2025] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:23 EDT 2025] IlluminaBasecallsToFastq --RUN_BARCODE HiMom --MACHINE_NAME machine1 --FLOWCELL_BARCODE abcdeACXX --MULTIPLEX_PARAMS /tmp/dualBarcode..dir2176444274401606870/barcode_double.params --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.5703261835070856070.metrics --MAX_RECORDS_IN_RAM 1000 --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --FORCE_GC true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --READ_NAME_FORMAT CASAVA_1_8 --MIN_TRIMMED_LENGTH 20 --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 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:23 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 13:01:23 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B8B25T
[Thu Apr 24 13:01:23 EDT 2025] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1503657984
[Thu Apr 24 13:01:24 EDT 2025] IlluminaBasecallsToFastq --OUTPUT_PREFIX /tmp/testMultiplexRH.dir5211122629195380136/testMultiplexRH --RUN_BARCODE HiMom --MACHINE_NAME machine1 --FLOWCELL_BARCODE abcdeACXX --READ_NAME_FORMAT ILLUMINA --LANE 1 --READ_STRUCTURE 25T8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --MAX_RECORDS_IN_RAM 100 --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --FORCE_GC true --SORT true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MATCH_BARCODES_INLINE false --MIN_TRIMMED_LENGTH 20 --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 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:24 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 13:01:24 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B25T
INFO 2025-04-24 13:01:24 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:01:24 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:01:24 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:01:24 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:01:24 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:01:24 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:01:24 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:01:24 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:01:24 EDT 2025] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:24 EDT 2025] IlluminaBasecallsToFastq --OUTPUT_PREFIX /tmp/nonBarcoded.12855333003958977131 --RUN_BARCODE HiMom --MACHINE_NAME machine1 --FLOWCELL_BARCODE abcdeACXX --LANE 1 --READ_STRUCTURE 25T8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --MAX_RECORDS_IN_RAM 100 --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --FORCE_GC true --SORT true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --READ_NAME_FORMAT CASAVA_1_8 --MATCH_BARCODES_INLINE false --MIN_TRIMMED_LENGTH 20 --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 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:24 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 13:01:24 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B25T
INFO 2025-04-24 13:01:24 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:01:24 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:01:24 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:01:24 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:01:24 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:01:24 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:01:24 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:01:24 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:01:24 EDT 2025] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:24 EDT 2025] IlluminaBasecallsToFastq --OUTPUT_PREFIX /tmp/qualityAdapterTrimmed.2077417858287975285 --RUN_BARCODE HiMom --MACHINE_NAME machine1 --FLOWCELL_BARCODE abcdeACXX --FIVE_PRIME_ADAPTER CGGCC --THREE_PRIME_ADAPTER TGGGC --TRIMMING_QUALITY 10 --LANE 1 --READ_STRUCTURE 25T8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --MAX_RECORDS_IN_RAM 100 --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --FORCE_GC true --SORT true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --READ_NAME_FORMAT CASAVA_1_8 --MATCH_BARCODES_INLINE false --MIN_TRIMMED_LENGTH 20 --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 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:01:24 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 13:01:24 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B25T
INFO 2025-04-24 13:01:24 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:01:24 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:01:24 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:01:24 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:01:24 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:01:25 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:01:25 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:01:25 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:01:25 EDT 2025] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:01:25 EDT 2025] IlluminaBasecallsToFastq --OUTPUT_PREFIX /tmp/qualityTrimmed.2416102696245246107 --RUN_BARCODE HiMom --MACHINE_NAME machine1 --FLOWCELL_BARCODE abcdeACXX --TRIMMING_QUALITY 10 --LANE 1 --READ_STRUCTURE 25T8B25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --MAX_RECORDS_IN_RAM 100 --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --FORCE_GC true --SORT true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --READ_NAME_FORMAT CASAVA_1_8 --MATCH_BARCODES_INLINE false --MIN_TRIMMED_LENGTH 20 --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 --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 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B25T
INFO 2025-04-24 13:01:25 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs
INFO 2025-04-24 13:01:25 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor
INFO 2025-04-24 13:01:25 SortedBasecallsConverter Tile 1101 Writer Executor Starting
INFO 2025-04-24 13:01:25 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor
INFO 2025-04-24 13:01:25 SortedBasecallsConverter Tile 1201 Writer Executor Starting
INFO 2025-04-24 13:01:25 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor
INFO 2025-04-24 13:01:25 SortedBasecallsConverter Tile 2101 Writer Executor Starting
INFO 2025-04-24 13:01:25 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor
[Thu Apr 24 13:01:25 EDT 2025] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824