Class picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest
Tests
| Test |
Duration |
Result |
| testEquivalence[0](false) |
0.016s |
passed |
| testEquivalence[1](true) |
0.014s |
passed |
Standard error
[Thu Apr 24 12:59:53 EDT 2025] CollectOxoGMetrics --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam --OUTPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/test3784057884723428959.oxo_g_metrics --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --MINIMUM_QUALITY_SCORE 20 --MINIMUM_MAPPING_QUALITY 30 --MINIMUM_INSERT_SIZE 60 --MAXIMUM_INSERT_SIZE 600 --INCLUDE_NON_PF_READS true --USE_OQ true --CONTEXT_SIZE 1 --STOP_AFTER 2147483647 --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 12:59:53 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 12:59:53 CollectOxoGMetrics Generated 16 context strings.
INFO 2025-04-24 12:59:53 CollectOxoGMetrics Loading dbSNP File: null
INFO 2025-04-24 12:59:53 CollectOxoGMetrics Starting iteration.
[Thu Apr 24 12:59:53 EDT 2025] picard.analysis.CollectOxoGMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 12:59:53 EDT 2025] CollectSequencingArtifactMetrics --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam --OUTPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/test6160351805225846295 --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --MINIMUM_QUALITY_SCORE 20 --MINIMUM_MAPPING_QUALITY 30 --MINIMUM_INSERT_SIZE 60 --MAXIMUM_INSERT_SIZE 600 --INCLUDE_UNPAIRED false --INCLUDE_DUPLICATES false --INCLUDE_NON_PF_READS false --TANDEM_READS false --USE_OQ true --CONTEXT_SIZE 1 --ASSUME_SORTED true --STOP_AFTER 0 --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 12:59:53 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 12:59:53 EDT 2025] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 12:59:53 EDT 2025] ConvertSequencingArtifactToOxoG --INPUT_BASE /mounts/lovelace/software/picard/picard/testdata/picard/sam/test6160351805225846295 --OUTPUT_BASE /mounts/lovelace/software/picard/picard/testdata/picard/sam/test7769064194032837733 --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 12:59:53 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 12:59:53 EDT 2025] picard.analysis.artifacts.ConvertSequencingArtifactToOxoG done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 12:59:53 EDT 2025] CollectOxoGMetrics --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam --OUTPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/test17578419806579518203.oxo_g_metrics --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --MINIMUM_QUALITY_SCORE 20 --MINIMUM_MAPPING_QUALITY 30 --MINIMUM_INSERT_SIZE 60 --MAXIMUM_INSERT_SIZE 600 --INCLUDE_NON_PF_READS true --USE_OQ true --CONTEXT_SIZE 1 --STOP_AFTER 2147483647 --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 12:59:53 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 12:59:53 CollectOxoGMetrics Generated 16 context strings.
INFO 2025-04-24 12:59:53 CollectOxoGMetrics Loading dbSNP File: null
INFO 2025-04-24 12:59:53 CollectOxoGMetrics Starting iteration.
[Thu Apr 24 12:59:53 EDT 2025] picard.analysis.CollectOxoGMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 12:59:53 EDT 2025] CollectSequencingArtifactMetrics --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam --OUTPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/test12297032350424844805 --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --MINIMUM_QUALITY_SCORE 20 --MINIMUM_MAPPING_QUALITY 30 --MINIMUM_INSERT_SIZE 60 --MAXIMUM_INSERT_SIZE 600 --INCLUDE_UNPAIRED false --INCLUDE_DUPLICATES false --INCLUDE_NON_PF_READS false --TANDEM_READS false --USE_OQ true --CONTEXT_SIZE 1 --ASSUME_SORTED true --STOP_AFTER 0 --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 12:59:53 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 12:59:53 EDT 2025] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 12:59:53 EDT 2025] ConvertSequencingArtifactToOxoG --PRE_ADAPTER_IN testdata/picard/sam/test12297032350424844805.pre_adapter_detail_metrics --BAIT_BIAS_IN testdata/picard/sam/test12297032350424844805.bait_bias_detail_metrics --OXOG_OUT testdata/picard/sam/test15539367616118401197.oxog_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 12:59:53 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 12:59:53 EDT 2025] picard.analysis.artifacts.ConvertSequencingArtifactToOxoG done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824