Class picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest
Tests
| Test |
Duration |
Result |
| testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam) |
0.010s |
passed |
| testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam) |
0.008s |
passed |
| testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam) |
0.007s |
passed |
| testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam) |
0.008s |
passed |
| testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam) |
0.008s |
passed |
| testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam) |
0.007s |
passed |
| testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam) |
0.007s |
passed |
| testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam) |
0.008s |
passed |
Standard error
[Thu Apr 24 13:17:35 EDT 2025] CollectDuplicateMetrics --METRICS_FILE /tmp/CollectDuplicateMetricsTester.tmp15996776267344646904/metrics.txt --INPUT /tmp/CollectDuplicateMetrics7778342215595509447.sam --ASSUME_SORTED true --STOP_AFTER 0 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:17:35 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
WARNING 2025-04-24 13:17:35 SinglePassSamProgram File reports sort order 'unknown', assuming it's coordinate sorted anyway.
[Thu Apr 24 13:17:35 EDT 2025] picard.sam.markduplicates.CollectDuplicateMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:17:35 EDT 2025] CollectDuplicateMetrics --METRICS_FILE /tmp/CollectDuplicateMetricsTester.tmp10527164270404566801/metrics.txt --INPUT /tmp/CollectDuplicateMetrics10934801531590131236.sam --ASSUME_SORTED true --STOP_AFTER 0 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:17:35 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
WARNING 2025-04-24 13:17:35 SinglePassSamProgram File reports sort order 'unknown', assuming it's coordinate sorted anyway.
[Thu Apr 24 13:17:35 EDT 2025] picard.sam.markduplicates.CollectDuplicateMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:17:35 EDT 2025] CollectDuplicateMetrics --METRICS_FILE /tmp/CollectDuplicateMetricsTester.tmp17522879484200814666/metrics.txt --INPUT /tmp/CollectDuplicateMetrics13326584362082937971.sam --ASSUME_SORTED true --STOP_AFTER 0 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:17:35 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
WARNING 2025-04-24 13:17:35 SinglePassSamProgram File reports sort order 'queryname', assuming it's coordinate sorted anyway.
[Thu Apr 24 13:17:35 EDT 2025] picard.sam.markduplicates.CollectDuplicateMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:17:35 EDT 2025] CollectDuplicateMetrics --METRICS_FILE /tmp/CollectDuplicateMetricsTester.tmp6514361837759060676/metrics.txt --INPUT /tmp/CollectDuplicateMetrics7519284461456762112.sam --ASSUME_SORTED true --STOP_AFTER 0 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:17:35 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
WARNING 2025-04-24 13:17:35 SinglePassSamProgram File reports sort order 'queryname', assuming it's coordinate sorted anyway.
[Thu Apr 24 13:17:35 EDT 2025] picard.sam.markduplicates.CollectDuplicateMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:17:35 EDT 2025] CollectDuplicateMetrics --METRICS_FILE /tmp/CollectDuplicateMetricsTester.tmp12882517248893097000/metrics.txt --INPUT /tmp/CollectDuplicateMetrics14356890852513175538.sam --ASSUME_SORTED true --STOP_AFTER 0 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:17:35 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 13:17:35 EDT 2025] picard.sam.markduplicates.CollectDuplicateMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:17:35 EDT 2025] CollectDuplicateMetrics --METRICS_FILE /tmp/CollectDuplicateMetricsTester.tmp1496485845031290140/metrics.txt --INPUT /tmp/CollectDuplicateMetrics8221745594761773140.sam --ASSUME_SORTED true --STOP_AFTER 0 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:17:35 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 13:17:35 EDT 2025] picard.sam.markduplicates.CollectDuplicateMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:17:35 EDT 2025] CollectDuplicateMetrics --METRICS_FILE /tmp/CollectDuplicateMetricsTester.tmp3952274977486360493/metrics.txt --INPUT /tmp/CollectDuplicateMetrics17737026630968992924.sam --ASSUME_SORTED true --STOP_AFTER 0 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:17:35 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 13:17:35 EDT 2025] picard.sam.markduplicates.CollectDuplicateMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:17:35 EDT 2025] CollectDuplicateMetrics --METRICS_FILE /tmp/CollectDuplicateMetricsTester.tmp6907982317115710695/metrics.txt --INPUT /tmp/CollectDuplicateMetrics4950108990008609258.sam --ASSUME_SORTED true --STOP_AFTER 0 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:17:35 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 13:17:35 EDT 2025] picard.sam.markduplicates.CollectDuplicateMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824