Class picard.illumina.CollectIlluminaBasecallingMetricsTest
Tests
| Test |
Duration |
Result |
| testIndexedRunLane1[0](true) |
0.008s |
passed |
| testIndexedRunLane1[1](false) |
0.004s |
passed |
| testNonIndexedRunLane1 |
0.010s |
passed |
| testNovaseqIndexedRun |
0.908s |
passed |
Standard error
[Thu Apr 24 13:00:35 EDT 2025] CollectIlluminaBasecallingMetrics --BASECALLS_DIR /tmp/cibm.tmp6475753667107682379/25T8B25T/Data/Intensities/BaseCalls --BARCODES_DIR /tmp/cibm.tmp6475753667107682379/25T8B25T/barcodes_dir --LANE 1 --INPUT /tmp/cibm.tmp6475753667107682379/25T8B25T/Data/Intensities/BaseCalls/barcodeData.1 --READ_STRUCTURE 25T8B25T --OUTPUT /tmp/cibm.15979966101611123013.metrics --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:35 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
[Thu Apr 24 13:00:35 EDT 2025] picard.illumina.CollectIlluminaBasecallingMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:35 EDT 2025] CollectIlluminaBasecallingMetrics --BASECALLS_DIR /tmp/cibm.tmp6475753667107682379/25T8B25T/Data/Intensities/BaseCalls --LANE 1 --INPUT /tmp/cibm.tmp6475753667107682379/25T8B25T/Data/Intensities/BaseCalls/barcodeData.1 --READ_STRUCTURE 25T8B25T --OUTPUT /tmp/cibm.7940317503903793589.metrics --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:35 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
[Thu Apr 24 13:00:35 EDT 2025] picard.illumina.CollectIlluminaBasecallingMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:35 EDT 2025] CollectIlluminaBasecallingMetrics --BASECALLS_DIR /tmp/cibm.tmp6475753667107682379/125T125T/Data/Intensities/BaseCalls --LANE 1 --READ_STRUCTURE 125T125T --OUTPUT /tmp/cibm.12243223091847353212.metrics --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:35 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
[Thu Apr 24 13:00:35 EDT 2025] picard.illumina.CollectIlluminaBasecallingMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:35 EDT 2025] CollectIlluminaBasecallingMetrics --BASECALLS_DIR testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls --LANE 1 --INPUT testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/barcodeData.1 --READ_STRUCTURE 151T8B8B151T --OUTPUT /tmp/cibm.5840267999582797780.metrics --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:35 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:35 CbclReader Processing tile 1101
INFO 2025-04-24 13:00:36 CbclReader Processing tile 1102
[Thu Apr 24 13:00:36 EDT 2025] picard.illumina.CollectIlluminaBasecallingMetrics done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1073741824