Class picard.illumina.IlluminaBasecallsToSamAdapterClippingTest
Tests
| Test |
Duration |
Result |
| testBasic[0](1, 125T125T) |
0.747s |
passed |
| testBasic[1](2, 125T125T) |
0.810s |
passed |
Standard output
Ouput Sam file is in /tmp/.1.illuminaBasecallsToSam1371587377552623021.sam
Ouput Sam file is in /tmp/.2.illuminaBasecallsToSam2696203895389307919.sam
Standard error
[Tue Aug 16 04:11:50 CDT 2016] picard.illumina.IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls LANE=1 OUTPUT=/tmp/.1.illuminaBasecallsToSam1371587377552623021.sam RUN_BARCODE=305PJAAXX080716 SAMPLE_ALIAS=myalias READ_STRUCTURE=125T125T SEQUENCING_CENTER=BI PLATFORM=illumina ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX 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 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 125T125T
INFO 2016-08-16 04:11:50 IlluminaBasecallsConverter All work is complete.
[Tue Aug 16 04:11:50 CDT 2016] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1776287744
[Tue Aug 16 04:11:50 CDT 2016] picard.illumina.IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls LANE=2 OUTPUT=/tmp/.2.illuminaBasecallsToSam2696203895389307919.sam RUN_BARCODE=305PJAAXX080716 SAMPLE_ALIAS=myalias READ_STRUCTURE=125T125T SEQUENCING_CENTER=BI PLATFORM=illumina ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX 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 04:11:51 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 125T125T
INFO 2016-08-16 04:11:51 IlluminaBasecallsConverter All work is complete.
[Tue Aug 16 04:11:51 CDT 2016] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1776287744