Class picard.illumina.IlluminaBasecallsToFastqTest
Tests
| Test |
Duration |
Result |
| testDeMultiplexed |
0.599s |
passed |
| testDeMultiplexedWithIndex |
0.642s |
passed |
| testDeMultiplexedWithtwoIndexes |
0.882s |
passed |
| testDualBarcodes |
0.750s |
passed |
| testMultiplexWithIlluminaReadNameHeaders |
0.082s |
passed |
| testNonBarcoded |
0.073s |
passed |
Standard error
[Tue Aug 16 04:11:47 CDT 2016] picard.illumina.IlluminaBasecallsToFastq BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom MACHINE_NAME=machine1 FLOWCELL_BARCODE=abcdeACXX READ_STRUCTURE=25T8B25T MULTIPLEX_PARAMS=/tmp/multiplexedBarcode.6117621278895085628.dir/mp_barcode.params MAX_READS_IN_RAM_PER_TILE=100 ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 APPLY_EAMSS_FILTER=true FORCE_GC=true MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false READ_NAME_FORMAT=CASAVA_1_8 COMPRESS_OUTPUTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:47 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO 2016-08-16 04:11:47 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B25T
INFO 2016-08-16 04:11:47 IlluminaBasecallsConverter All work is complete.
INFO 2016-08-16 04:11:47 IlluminaBasecallsConverter All work is complete.
[Tue Aug 16 04:11:47 CDT 2016] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1826619392
[Tue Aug 16 04:11:47 CDT 2016] picard.illumina.IlluminaBasecallsToFastq BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom MACHINE_NAME=machine1 FLOWCELL_BARCODE=abcdeACXX READ_STRUCTURE=25T8B4M21T MULTIPLEX_PARAMS=/tmp/multiplexedBarcodeWithIndex.7593611231749783252.dir/mp_barcode.params MAX_READS_IN_RAM_PER_TILE=100 ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 APPLY_EAMSS_FILTER=true FORCE_GC=true MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false READ_NAME_FORMAT=CASAVA_1_8 COMPRESS_OUTPUTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:47 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO 2016-08-16 04:11:47 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B4M21T
INFO 2016-08-16 04:11:47 IlluminaBasecallsConverter All work is complete.
[Tue Aug 16 04:11:47 CDT 2016] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1773142016
[Tue Aug 16 04:11:48 CDT 2016] picard.illumina.IlluminaBasecallsToFastq BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom MACHINE_NAME=machine1 FLOWCELL_BARCODE=abcdeACXX READ_STRUCTURE=25T8B4M4M17T MULTIPLEX_PARAMS=/tmp/multiplexedBarcodeWithTwoIndexes.7515270649422633741.dir/mp_barcode.params MAX_READS_IN_RAM_PER_TILE=100 ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 APPLY_EAMSS_FILTER=true FORCE_GC=true MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false READ_NAME_FORMAT=CASAVA_1_8 COMPRESS_OUTPUTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:48 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO 2016-08-16 04:11:48 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B4M4M17T
INFO 2016-08-16 04:11:48 IlluminaBasecallsConverter All work is complete.
[Tue Aug 16 04:11:48 CDT 2016] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1799880704
[Tue Aug 16 04:11:49 CDT 2016] picard.illumina.IlluminaBasecallsToFastq BASECALLS_DIR=testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom MACHINE_NAME=machine1 FLOWCELL_BARCODE=abcdeACXX READ_STRUCTURE=25T8B8B25T MULTIPLEX_PARAMS=/tmp/dualBarcode.4335482929816706802.dir/barcode_double.params MAX_READS_IN_RAM_PER_TILE=100 ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 APPLY_EAMSS_FILTER=true FORCE_GC=true MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false READ_NAME_FORMAT=CASAVA_1_8 COMPRESS_OUTPUTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:49 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO 2016-08-16 04:11:49 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B8B25T
INFO 2016-08-16 04:11:49 IlluminaBasecallsConverter All work is complete.
[Tue Aug 16 04:11:49 CDT 2016] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1752694784
[Tue Aug 16 04:11:50 CDT 2016] picard.illumina.IlluminaBasecallsToFastq BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 OUTPUT_PREFIX=/tmp/testMultiplexRH.441261026209968559.dir/testMultiplexRH RUN_BARCODE=HiMom MACHINE_NAME=machine1 FLOWCELL_BARCODE=abcdeACXX READ_STRUCTURE=25T8B25T MAX_READS_IN_RAM_PER_TILE=100 READ_NAME_FORMAT=ILLUMINA ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 APPLY_EAMSS_FILTER=true FORCE_GC=true MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false COMPRESS_OUTPUTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:50 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO 2016-08-16 04:11:50 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B25T
INFO 2016-08-16 04:11:50 IlluminaBasecallsConverter All work is complete.
[Tue Aug 16 04:11:50 CDT 2016] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1776287744
[Tue Aug 16 04:11:50 CDT 2016] picard.illumina.IlluminaBasecallsToFastq BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 OUTPUT_PREFIX=/tmp/nonBarcoded.587302985851493043 RUN_BARCODE=HiMom MACHINE_NAME=machine1 FLOWCELL_BARCODE=abcdeACXX READ_STRUCTURE=25T8B25T MAX_READS_IN_RAM_PER_TILE=100 ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 APPLY_EAMSS_FILTER=true FORCE_GC=true MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false READ_NAME_FORMAT=CASAVA_1_8 COMPRESS_OUTPUTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:50 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO 2016-08-16 04:11:50 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B25T
INFO 2016-08-16 04:11:50 IlluminaBasecallsConverter All work is complete.
[Tue Aug 16 04:11:50 CDT 2016] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1776287744