Class picard.analysis.CollectGcBiasMetricsTest

INFO	2025-04-24 12:59:15	RExecutor	Executing R script via command: Rscript /tmp/script13201006133073186399.R
INFO	2025-04-24 12:59:15	ProcessExecutor	[1] "Checking if R is installed"
[Thu Apr 24 12:59:15 EDT 2025] CollectGcBiasMetrics --CHART_OUTPUT /tmp/test9994929316833054289.pdf --SUMMARY_OUTPUT /tmp/test3866088138372291561.gc_bias.summary_metrics --SCAN_WINDOW_SIZE 100 --MINIMUM_GENOME_FRACTION 1.0E-5 --IS_BISULFITE_SEQUENCED false --METRIC_ACCUMULATION_LEVEL ALL_READS --METRIC_ACCUMULATION_LEVEL SAMPLE --METRIC_ACCUMULATION_LEVEL READ_GROUP --ALSO_IGNORE_DUPLICATES false --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/metrics/chrM_NO_SEQ.sam --OUTPUT /tmp/test12798417821088702405.gc_bias.detail_metrics --ASSUME_SORTED false --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --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 12:59:15 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 12:59:15	GcBiasMetricsCollector	Omitting read NRUSCA-WDL30341:66:000000000-ABTGC:1:2111:13507:4770 with '*' in SEQ field.
WARNING	2025-04-24 12:59:15	GcBiasMetricsCollector	Omitting read NRUSCA-WDL30341:66:000000000-ABTGC:1:2111:13507:4770 with '*' in SEQ field.
WARNING	2025-04-24 12:59:15	GcBiasMetricsCollector	Omitting read NRUSCA-WDL30341:66:000000000-ABTGC:1:2111:13507:4770 with '*' in SEQ field.
INFO	2025-04-24 12:59:15	RExecutor	Executing R script via command: Rscript /tmp/script8963845099276369038.R /tmp/test12798417821088702405.gc_bias.detail_metrics /tmp/test3866088138372291561.gc_bias.summary_metrics /tmp/test9994929316833054289.pdf 100
INFO	2025-04-24 12:59:15	ProcessExecutor	Total clusters:  0 , Aligned reads:  1Total clusters:  0 , Aligned reads:  1Total clusters:  0 , Aligned reads:  1
[Thu Apr 24 12:59:15 EDT 2025] picard.analysis.CollectGcBiasMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
INFO	2025-04-24 12:59:15	RExecutor	Executing R script via command: Rscript /tmp/script8146926276864380900.R
INFO	2025-04-24 12:59:15	ProcessExecutor	[1] "Checking if R is installed"
[Thu Apr 24 12:59:15 EDT 2025] CollectGcBiasMetrics --CHART_OUTPUT /tmp/test9712968851806239230.pdf --SUMMARY_OUTPUT /tmp/test5516604588804578015.gc_bias.summary_metrics --SCAN_WINDOW_SIZE 100 --MINIMUM_GENOME_FRACTION 1.0E-5 --IS_BISULFITE_SEQUENCED false --METRIC_ACCUMULATION_LEVEL ALL_READS --METRIC_ACCUMULATION_LEVEL SAMPLE --METRIC_ACCUMULATION_LEVEL READ_GROUP --ALSO_IGNORE_DUPLICATES false --INPUT /tmp/CollectGcBias3092200578408635302.bam --OUTPUT /tmp/test14676905009191127102.gc_bias.detail_metrics --ASSUME_SORTED false --REFERENCE_SEQUENCE testdata/picard/metrics/chrMNO.reference.fasta --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 12:59:15 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 12:59:15	RExecutor	Executing R script via command: Rscript /tmp/script330718707963088276.R /tmp/test14676905009191127102.gc_bias.detail_metrics /tmp/test5516604588804578015.gc_bias.summary_metrics /tmp/test9712968851806239230.pdf 100
INFO	2025-04-24 12:59:16	ProcessExecutor	Total clusters:  300 , Aligned reads:  600Total clusters:  200 , Aligned reads:  400Total clusters:  100 , Aligned reads:  200Total clusters:  100 , Aligned reads:  200Total clusters:  100 , Aligned reads:  200Total clusters:  100 , Aligned reads:  200
[Thu Apr 24 12:59:16 EDT 2025] picard.analysis.CollectGcBiasMetrics done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824
INFO	2025-04-24 12:59:16	RExecutor	Executing R script via command: Rscript /tmp/script6830269282394529939.R
INFO	2025-04-24 12:59:16	ProcessExecutor	[1] "Checking if R is installed"
[Thu Apr 24 12:59:16 EDT 2025] CollectGcBiasMetrics --CHART_OUTPUT /tmp/test18363911525043078838.pdf --SUMMARY_OUTPUT /tmp/test17667081076750732321.gc_bias_summary_metrics --SCAN_WINDOW_SIZE 100 --MINIMUM_GENOME_FRACTION 1.0E-5 --IS_BISULFITE_SEQUENCED false --METRIC_ACCUMULATION_LEVEL ALL_READS --METRIC_ACCUMULATION_LEVEL SAMPLE --METRIC_ACCUMULATION_LEVEL READ_GROUP --ALSO_IGNORE_DUPLICATES true --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/metrics/chrMReads.sam --OUTPUT /tmp/test2705215476514439281.gc_bias_detail_metrics --ASSUME_SORTED false --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --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 12:59:16 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 12:59:16	RExecutor	Executing R script via command: Rscript /tmp/script2565156338108355266.R /tmp/test2705215476514439281.gc_bias_detail_metrics /tmp/test17667081076750732321.gc_bias_summary_metrics /tmp/test18363911525043078838.pdf 100
INFO	2025-04-24 12:59:16	ProcessExecutor	Total clusters:  5 , Aligned reads:  5Total clusters:  3 , Aligned reads:  3Total clusters:  5 , Aligned reads:  5Total clusters:  3 , Aligned reads:  3Total clusters:  5 , Aligned reads:  5Total clusters:  3 , Aligned reads:  3
[Thu Apr 24 12:59:16 EDT 2025] picard.analysis.CollectGcBiasMetrics done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824
INFO	2025-04-24 12:59:16	RExecutor	Executing R script via command: Rscript /tmp/script27366017163873280.R
INFO	2025-04-24 12:59:16	ProcessExecutor	[1] "Checking if R is installed"
[Thu Apr 24 12:59:16 EDT 2025] CollectGcBiasMetrics --CHART_OUTPUT /tmp/test3799978043805962603.pdf --SUMMARY_OUTPUT /tmp/test3549265837883094932.gc_bias_summary_metrics --SCAN_WINDOW_SIZE 100 --MINIMUM_GENOME_FRACTION 1.0E-5 --IS_BISULFITE_SEQUENCED false --METRIC_ACCUMULATION_LEVEL ALL_READS --METRIC_ACCUMULATION_LEVEL SAMPLE --METRIC_ACCUMULATION_LEVEL READ_GROUP --ALSO_IGNORE_DUPLICATES false --INPUT /tmp/CollectGcBias3092200578408635302.bam --OUTPUT /tmp/test3385955244566492566.gc_bias_detail_metrics --ASSUME_SORTED false --REFERENCE_SEQUENCE testdata/picard/metrics/chrMNO.reference.fasta --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 12:59:16 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 12:59:16	RExecutor	Executing R script via command: Rscript /tmp/script16628992312124913980.R /tmp/test3385955244566492566.gc_bias_detail_metrics /tmp/test3549265837883094932.gc_bias_summary_metrics /tmp/test3799978043805962603.pdf 100
INFO	2025-04-24 12:59:17	ProcessExecutor	Total clusters:  300 , Aligned reads:  600Total clusters:  200 , Aligned reads:  400Total clusters:  100 , Aligned reads:  200Total clusters:  100 , Aligned reads:  200Total clusters:  100 , Aligned reads:  200Total clusters:  100 , Aligned reads:  200
[Thu Apr 24 12:59:17 EDT 2025] picard.analysis.CollectGcBiasMetrics done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824
INFO	2025-04-24 12:59:17	RExecutor	Executing R script via command: Rscript /tmp/script2595448818757805984.R
INFO	2025-04-24 12:59:17	ProcessExecutor	[1] "Checking if R is installed"
[Thu Apr 24 12:59:17 EDT 2025] CollectGcBiasMetrics --CHART_OUTPUT /tmp/test12411207498047813881.pdf --SUMMARY_OUTPUT /tmp/testAllChr16134363230660534582.gc_bias_summary_metrics --SCAN_WINDOW_SIZE 100 --MINIMUM_GENOME_FRACTION 1.0E-5 --IS_BISULFITE_SEQUENCED false --METRIC_ACCUMULATION_LEVEL ALL_READS --METRIC_ACCUMULATION_LEVEL SAMPLE --METRIC_ACCUMULATION_LEVEL READ_GROUP --ALSO_IGNORE_DUPLICATES false --INPUT /tmp/CollectGcBias18101406139594151109.bam --OUTPUT /tmp/testAllChrDetails4595305865812353209.gc_bias_detail_metrics --ASSUME_SORTED false --REFERENCE_SEQUENCE testdata/picard/metrics/chrMNO.reference.fasta --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 12:59:17 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 12:59:17	RExecutor	Executing R script via command: Rscript /tmp/script16325093595959777226.R /tmp/testAllChrDetails4595305865812353209.gc_bias_detail_metrics /tmp/testAllChr16134363230660534582.gc_bias_summary_metrics /tmp/test12411207498047813881.pdf 100
INFO	2025-04-24 12:59:17	ProcessExecutor	Total clusters:  100 , Aligned reads:  200Total clusters:  100 , Aligned reads:  200Total clusters:  100 , Aligned reads:  200
[Thu Apr 24 12:59:17 EDT 2025] picard.analysis.CollectGcBiasMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824