Class picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest
Tests
| Test |
Duration |
Result |
| testNoCoverage |
2.220s |
passed |
| testPoorQualityBases |
0.841s |
passed |
| testWithIntervals |
2.882s |
passed |
| testWithoutIntervals |
2.830s |
passed |
Standard error
INFO 2025-04-24 12:59:34 RExecutor Executing R script via command: Rscript /tmp/script10689487159848817576.R
INFO 2025-04-24 12:59:34 ProcessExecutor [1] "Checking if R is installed"
[Thu Apr 24 12:59:34 EDT 2025] CollectWgsMetricsWithNonZeroCoverage --CHART_OUTPUT /tmp/testPoorQualityBases12741862514532270937.pdf --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/CollectWgsMetrics8240078952871414412.bam --OUTPUT /tmp/testPoorQualityBases-metrics9294284663525383775.txt --COVERAGE_CAP 3 --INCLUDE_BQ_HISTOGRAM true --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --LOCUS_ACCUMULATION_CAP 100000 --STOP_AFTER -1 --COUNT_UNPAIRED false --SAMPLE_SIZE 10000 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --USE_FAST_ALGORITHM false --READ_LENGTH 150 --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 12:59:34 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 12:59:34 AbstractLocusIterator SamLocusIterator constructed with samReader that has SortOrder == unsorted. Assuming SAM is coordinate sorted, but exceptions may occur if it is not.
INFO 2025-04-24 12:59:34 TheoreticalSensitivity Creating Roulette Wheel
INFO 2025-04-24 12:59:34 TheoreticalSensitivity Calculating quality sums from quality sampler
INFO 2025-04-24 12:59:34 TheoreticalSensitivity 0 sampling iterations completed
INFO 2025-04-24 12:59:34 TheoreticalSensitivity 1000 sampling iterations completed
INFO 2025-04-24 12:59:34 TheoreticalSensitivity 2000 sampling iterations completed
INFO 2025-04-24 12:59:34 TheoreticalSensitivity 3000 sampling iterations completed
INFO 2025-04-24 12:59:34 TheoreticalSensitivity 4000 sampling iterations completed
INFO 2025-04-24 12:59:34 TheoreticalSensitivity 5000 sampling iterations completed
INFO 2025-04-24 12:59:35 TheoreticalSensitivity 6000 sampling iterations completed
INFO 2025-04-24 12:59:35 TheoreticalSensitivity 7000 sampling iterations completed
INFO 2025-04-24 12:59:35 TheoreticalSensitivity 8000 sampling iterations completed
INFO 2025-04-24 12:59:35 TheoreticalSensitivity 9000 sampling iterations completed
INFO 2025-04-24 12:59:35 TheoreticalSensitivity Calculating theoretical het sensitivity
INFO 2025-04-24 12:59:35 TheoreticalSensitivity Creating Roulette Wheel
INFO 2025-04-24 12:59:35 TheoreticalSensitivity Calculating quality sums from quality sampler
INFO 2025-04-24 12:59:35 TheoreticalSensitivity 0 sampling iterations completed
INFO 2025-04-24 12:59:35 TheoreticalSensitivity 1000 sampling iterations completed
INFO 2025-04-24 12:59:35 TheoreticalSensitivity 2000 sampling iterations completed
INFO 2025-04-24 12:59:35 TheoreticalSensitivity 3000 sampling iterations completed
INFO 2025-04-24 12:59:35 TheoreticalSensitivity 4000 sampling iterations completed
INFO 2025-04-24 12:59:35 TheoreticalSensitivity 5000 sampling iterations completed
INFO 2025-04-24 12:59:35 TheoreticalSensitivity 6000 sampling iterations completed
INFO 2025-04-24 12:59:36 TheoreticalSensitivity 7000 sampling iterations completed
INFO 2025-04-24 12:59:36 TheoreticalSensitivity 8000 sampling iterations completed
INFO 2025-04-24 12:59:36 TheoreticalSensitivity 9000 sampling iterations completed
INFO 2025-04-24 12:59:36 TheoreticalSensitivity Calculating theoretical het sensitivity
INFO 2025-04-24 12:59:36 RExecutor Executing R script via command: Rscript /tmp/script9217497314669518146.R /tmp/testPoorQualityBases-metrics9294284663525383775.txt /tmp/testPoorQualityBases12741862514532270937.pdf CollectWgsMetrics8240078952871414412.bam TestLibrary1
ERROR 2025-04-24 12:59:36 ProcessExecutor Warning message:
ERROR 2025-04-24 12:59:36 ProcessExecutor In as.numeric(metrics$MEAN_COVERAGE[i]) : NAs introduced by coercion
INFO 2025-04-24 12:59:36 ProcessExecutor null device
INFO 2025-04-24 12:59:36 ProcessExecutor 1
[Thu Apr 24 12:59:36 EDT 2025] picard.analysis.CollectWgsMetricsWithNonZeroCoverage done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=1073741824
INFO 2025-04-24 12:59:36 RExecutor Executing R script via command: Rscript /tmp/script8505910999859155943.R
INFO 2025-04-24 12:59:36 ProcessExecutor [1] "Checking if R is installed"
[Thu Apr 24 12:59:36 EDT 2025] CollectWgsMetricsWithNonZeroCoverage --CHART_OUTPUT /tmp/testExcludedBases18149835263003825533.pdf --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/CollectWgsMetrics11038400969268101659.bam --OUTPUT /tmp/testExcludedBases-metrics6961460278613144088.txt --COVERAGE_CAP 3 --INCLUDE_BQ_HISTOGRAM true --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --LOCUS_ACCUMULATION_CAP 100000 --STOP_AFTER -1 --COUNT_UNPAIRED false --SAMPLE_SIZE 10000 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --USE_FAST_ALGORITHM false --READ_LENGTH 150 --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 12:59:36 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 12:59:36 AbstractLocusIterator SamLocusIterator constructed with samReader that has SortOrder == unsorted. Assuming SAM is coordinate sorted, but exceptions may occur if it is not.
INFO 2025-04-24 12:59:36 TheoreticalSensitivity Creating Roulette Wheel
INFO 2025-04-24 12:59:36 TheoreticalSensitivity Calculating quality sums from quality sampler
INFO 2025-04-24 12:59:36 TheoreticalSensitivity 0 sampling iterations completed
INFO 2025-04-24 12:59:36 TheoreticalSensitivity 1000 sampling iterations completed
INFO 2025-04-24 12:59:36 TheoreticalSensitivity 2000 sampling iterations completed
INFO 2025-04-24 12:59:36 TheoreticalSensitivity 3000 sampling iterations completed
INFO 2025-04-24 12:59:36 TheoreticalSensitivity 4000 sampling iterations completed
INFO 2025-04-24 12:59:36 TheoreticalSensitivity 5000 sampling iterations completed
INFO 2025-04-24 12:59:36 TheoreticalSensitivity 6000 sampling iterations completed
INFO 2025-04-24 12:59:36 TheoreticalSensitivity 7000 sampling iterations completed
INFO 2025-04-24 12:59:36 TheoreticalSensitivity 8000 sampling iterations completed
INFO 2025-04-24 12:59:36 TheoreticalSensitivity 9000 sampling iterations completed
INFO 2025-04-24 12:59:36 TheoreticalSensitivity Calculating theoretical het sensitivity
INFO 2025-04-24 12:59:36 TheoreticalSensitivity Creating Roulette Wheel
INFO 2025-04-24 12:59:36 TheoreticalSensitivity Calculating quality sums from quality sampler
INFO 2025-04-24 12:59:36 TheoreticalSensitivity 0 sampling iterations completed
INFO 2025-04-24 12:59:36 TheoreticalSensitivity 1000 sampling iterations completed
INFO 2025-04-24 12:59:36 TheoreticalSensitivity 2000 sampling iterations completed
INFO 2025-04-24 12:59:36 TheoreticalSensitivity 3000 sampling iterations completed
INFO 2025-04-24 12:59:37 TheoreticalSensitivity 4000 sampling iterations completed
INFO 2025-04-24 12:59:37 TheoreticalSensitivity 5000 sampling iterations completed
INFO 2025-04-24 12:59:37 TheoreticalSensitivity 6000 sampling iterations completed
INFO 2025-04-24 12:59:37 TheoreticalSensitivity 7000 sampling iterations completed
INFO 2025-04-24 12:59:37 TheoreticalSensitivity 8000 sampling iterations completed
INFO 2025-04-24 12:59:37 TheoreticalSensitivity 9000 sampling iterations completed
INFO 2025-04-24 12:59:37 TheoreticalSensitivity Calculating theoretical het sensitivity
INFO 2025-04-24 12:59:37 RExecutor Executing R script via command: Rscript /tmp/script11434311344647421806.R /tmp/testExcludedBases-metrics6961460278613144088.txt /tmp/testExcludedBases18149835263003825533.pdf CollectWgsMetrics11038400969268101659.bam TestLibrary1
INFO 2025-04-24 12:59:37 ProcessExecutor null device
INFO 2025-04-24 12:59:37 ProcessExecutor 1
[Thu Apr 24 12:59:37 EDT 2025] picard.analysis.CollectWgsMetricsWithNonZeroCoverage done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824
INFO 2025-04-24 12:59:37 RExecutor Executing R script via command: Rscript /tmp/script1264728973835306524.R
INFO 2025-04-24 12:59:37 ProcessExecutor [1] "Checking if R is installed"
[Thu Apr 24 12:59:37 EDT 2025] CollectWgsMetricsWithNonZeroCoverage --CHART_OUTPUT /tmp/test9847257354073448908.wgs_metrics.pdf --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/forMetrics.sam --OUTPUT /tmp/test14761456164337239675.wgs_metrics --SAMPLE_SIZE 1000 --INTERVALS /mounts/lovelace/software/picard/picard/testdata/picard/sam/largeIntervals.interval_list --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --COVERAGE_CAP 250 --LOCUS_ACCUMULATION_CAP 100000 --STOP_AFTER -1 --INCLUDE_BQ_HISTOGRAM false --COUNT_UNPAIRED false --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --USE_FAST_ALGORITHM false --READ_LENGTH 150 --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 12:59:37 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 12:59:37 TheoreticalSensitivity Creating Roulette Wheel
INFO 2025-04-24 12:59:37 TheoreticalSensitivity Calculating quality sums from quality sampler
INFO 2025-04-24 12:59:37 TheoreticalSensitivity 0 sampling iterations completed
INFO 2025-04-24 12:59:38 TheoreticalSensitivity Calculating theoretical het sensitivity
INFO 2025-04-24 12:59:38 TheoreticalSensitivity Creating Roulette Wheel
INFO 2025-04-24 12:59:38 TheoreticalSensitivity Calculating quality sums from quality sampler
INFO 2025-04-24 12:59:38 TheoreticalSensitivity 0 sampling iterations completed
INFO 2025-04-24 12:59:39 TheoreticalSensitivity Calculating theoretical het sensitivity
INFO 2025-04-24 12:59:39 RExecutor Executing R script via command: Rscript /tmp/script11780443739494750336.R /tmp/test14761456164337239675.wgs_metrics /tmp/test9847257354073448908.wgs_metrics.pdf forMetrics.sam
INFO 2025-04-24 12:59:40 ProcessExecutor null device
INFO 2025-04-24 12:59:40 ProcessExecutor 1
[Thu Apr 24 12:59:40 EDT 2025] picard.analysis.CollectWgsMetricsWithNonZeroCoverage done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=1073741824
INFO 2025-04-24 12:59:40 RExecutor Executing R script via command: Rscript /tmp/script11997871027839757613.R
INFO 2025-04-24 12:59:40 ProcessExecutor [1] "Checking if R is installed"
[Thu Apr 24 12:59:40 EDT 2025] CollectWgsMetricsWithNonZeroCoverage --CHART_OUTPUT /tmp/test10739996861673284338.wgs_metrics.pdf --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/forMetrics.sam --OUTPUT /tmp/test13823491673790888973.wgs_metrics --SAMPLE_SIZE 1000 --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --COVERAGE_CAP 250 --LOCUS_ACCUMULATION_CAP 100000 --STOP_AFTER -1 --INCLUDE_BQ_HISTOGRAM false --COUNT_UNPAIRED false --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --USE_FAST_ALGORITHM false --READ_LENGTH 150 --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 12:59:40 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 12:59:40 TheoreticalSensitivity Creating Roulette Wheel
INFO 2025-04-24 12:59:40 TheoreticalSensitivity Calculating quality sums from quality sampler
INFO 2025-04-24 12:59:40 TheoreticalSensitivity 0 sampling iterations completed
INFO 2025-04-24 12:59:41 TheoreticalSensitivity Calculating theoretical het sensitivity
INFO 2025-04-24 12:59:41 TheoreticalSensitivity Creating Roulette Wheel
INFO 2025-04-24 12:59:41 TheoreticalSensitivity Calculating quality sums from quality sampler
INFO 2025-04-24 12:59:41 TheoreticalSensitivity 0 sampling iterations completed
INFO 2025-04-24 12:59:42 TheoreticalSensitivity Calculating theoretical het sensitivity
INFO 2025-04-24 12:59:42 RExecutor Executing R script via command: Rscript /tmp/script11539182809325463454.R /tmp/test13823491673790888973.wgs_metrics /tmp/test10739996861673284338.wgs_metrics.pdf forMetrics.sam
INFO 2025-04-24 12:59:43 ProcessExecutor null device
INFO 2025-04-24 12:59:43 ProcessExecutor 1
[Thu Apr 24 12:59:43 EDT 2025] picard.analysis.CollectWgsMetricsWithNonZeroCoverage done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=1073741824