Class picard.analysis.CollectMultipleMetricsTest
Tests
| Test |
Duration |
Result |
| testAlignmentSummaryViaMultipleMetrics |
0.660s |
passed |
| testGcBiasMetrics |
0.967s |
passed |
| testInsertSize |
0.640s |
passed |
| testMultipleMetricsFailing[0](BLAH::HISTOGRAM_WIDTH=58) |
0.180s |
passed |
| testMultipleMetricsFailing[1](QualityScoreDistribution::HISTOGRAM_WIDTH=58) |
0.172s |
passed |
| testMultipleMetricsFailing[2](CollectInsertSizeMetrics::BLAH=58) |
0.183s |
passed |
| testMultipleMetricsFailing[3](CollectInsertSizeMetrics:HISTOGRAM_WIDTH=58) |
0.174s |
passed |
| testMultipleMetricsFailing[4](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8) |
0.169s |
passed |
| testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=) |
0.167s |
passed |
| testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello) |
0.173s |
passed |
| testMultipleMetricsFailing[7](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta) |
0.162s |
passed |
| testMultipleMetricsFailing[8](CollectInsertSizeMetrics::OUTPUT=) |
0.174s |
passed |
| testRnaSeqMetricsViaMultipleMetrics |
1.304s |
passed |
Standard error
INFO 2025-04-24 12:59:19 RExecutor Executing R script via command: Rscript /tmp/script14119448005305287882.R
INFO 2025-04-24 12:59:19 ProcessExecutor [1] "Checking if R is installed"
[Thu Apr 24 12:59:19 EDT 2025] CollectMultipleMetrics --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam --OUTPUT /tmp/alignmentMetrics5594951775211717803 --METRIC_ACCUMULATION_LEVEL ALL_READS --PROGRAM CollectAlignmentSummaryMetrics --PROGRAM CollectInsertSizeMetrics --EXTRA_ARGUMENT CollectInsertSizeMetrics::--HISTOGRAM_WIDTH 58 --EXTRA_ARGUMENT CollectInsertSizeMetrics::--METRIC_ACCUMULATION_LEVEL LIBRARY --EXTRA_ARGUMENT CollectInsertSizeMetrics::--METRIC_ACCUMULATION_LEVEL READ_GROUP --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.fasta --ASSUME_SORTED true --STOP_AFTER 0 --INCLUDE_UNPAIRED false --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 12:59:19 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 12:59:19 RExecutor Executing R script via command: Rscript /tmp/script3004520427285662805.R /tmp/alignmentMetrics5594951775211717803.alignment_summary_metrics /tmp/alignmentMetrics5594951775211717803.read_length_histogram.pdf summary_alignment_stats_test.sam
INFO 2025-04-24 12:59:19 ProcessExecutor null device
INFO 2025-04-24 12:59:19 ProcessExecutor 1
INFO 2025-04-24 12:59:19 RExecutor Executing R script via command: Rscript /tmp/script130034364999682416.R /tmp/alignmentMetrics5594951775211717803.insert_size_metrics /tmp/alignmentMetrics5594951775211717803.insert_size_histogram.pdf summary_alignment_stats_test.sam 58
INFO 2025-04-24 12:59:20 ProcessExecutor null device
INFO 2025-04-24 12:59:20 ProcessExecutor 1
[Thu Apr 24 12:59:20 EDT 2025] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824
INFO 2025-04-24 12:59:20 RExecutor Executing R script via command: Rscript /tmp/script2724672913408056131.R
INFO 2025-04-24 12:59:20 ProcessExecutor [1] "Checking if R is installed"
[Thu Apr 24 12:59:20 EDT 2025] CollectMultipleMetrics --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/CollectGcBiasMetrics/CollectGcBias15854201712113585479.bam --OUTPUT /tmp/test9279844380957044201 --METRIC_ACCUMULATION_LEVEL ALL_READS --PROGRAM CollectAlignmentSummaryMetrics --PROGRAM CollectInsertSizeMetrics --PROGRAM CollectGcBiasMetrics --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --ASSUME_SORTED true --STOP_AFTER 0 --INCLUDE_UNPAIRED false --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 12:59:20 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 12:59:20 RExecutor Executing R script via command: Rscript /tmp/script17702308595270351056.R /tmp/test9279844380957044201.alignment_summary_metrics /tmp/test9279844380957044201.read_length_histogram.pdf CollectGcBias15854201712113585479.bam
INFO 2025-04-24 12:59:20 ProcessExecutor null device
INFO 2025-04-24 12:59:20 ProcessExecutor 1
INFO 2025-04-24 12:59:20 RExecutor Executing R script via command: Rscript /tmp/script2184261771852666122.R /tmp/test9279844380957044201.insert_size_metrics /tmp/test9279844380957044201.insert_size_histogram.pdf CollectGcBias15854201712113585479.bam
INFO 2025-04-24 12:59:20 ProcessExecutor null device
INFO 2025-04-24 12:59:20 ProcessExecutor 1
INFO 2025-04-24 12:59:20 RExecutor Executing R script via command: Rscript /tmp/script17697437744081529063.R /tmp/test9279844380957044201.gc_bias.detail_metrics /tmp/test9279844380957044201.gc_bias.summary_metrics /tmp/test9279844380957044201.gc_bias.pdf 100
INFO 2025-04-24 12:59:21 ProcessExecutor Total clusters: 300 , Aligned reads: 600
[Thu Apr 24 12:59:21 EDT 2025] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824
INFO 2025-04-24 12:59:21 RExecutor Executing R script via command: Rscript /tmp/script9987072344119252149.R
INFO 2025-04-24 12:59:21 ProcessExecutor [1] "Checking if R is installed"
[Thu Apr 24 12:59:21 EDT 2025] CollectMultipleMetrics --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/insert_size_metrics_test.sam --OUTPUT /tmp/test17504251464609316725 --METRIC_ACCUMULATION_LEVEL ALL_READS --PROGRAM CollectAlignmentSummaryMetrics --PROGRAM CollectInsertSizeMetrics --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.fasta --ASSUME_SORTED true --STOP_AFTER 0 --INCLUDE_UNPAIRED false --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 12:59:21 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 12:59:21 RExecutor Executing R script via command: Rscript /tmp/script16196949201314574824.R /tmp/test17504251464609316725.alignment_summary_metrics /tmp/test17504251464609316725.read_length_histogram.pdf insert_size_metrics_test.sam
INFO 2025-04-24 12:59:21 ProcessExecutor null device
INFO 2025-04-24 12:59:21 ProcessExecutor 1
INFO 2025-04-24 12:59:21 RExecutor Executing R script via command: Rscript /tmp/script17326573868528855820.R /tmp/test17504251464609316725.insert_size_metrics /tmp/test17504251464609316725.insert_size_histogram.pdf insert_size_metrics_test.sam
INFO 2025-04-24 12:59:21 ProcessExecutor null device
INFO 2025-04-24 12:59:21 ProcessExecutor 1
[Thu Apr 24 12:59:21 EDT 2025] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824
INFO 2025-04-24 12:59:21 RExecutor Executing R script via command: Rscript /tmp/script11347011458139014906.R
INFO 2025-04-24 12:59:21 ProcessExecutor [1] "Checking if R is installed"
[Thu Apr 24 12:59:21 EDT 2025] CollectMultipleMetrics --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/summary_alignment_stats_test.sam --OUTPUT /tmp/alignmentMetrics2720632981166406661 --METRIC_ACCUMULATION_LEVEL ALL_READS --PROGRAM CollectAlignmentSummaryMetrics --PROGRAM CollectInsertSizeMetrics --EXTRA_ARGUMENT BLAH::--HISTOGRAM_WIDTH 58 --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/summary_alignment_stats_test.fasta --ASSUME_SORTED true --STOP_AFTER 0 --INCLUDE_UNPAIRED false --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 12:59:21 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 12:59:21 EDT 2025] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
INFO 2025-04-24 12:59:21 RExecutor Executing R script via command: Rscript /tmp/script12408011063903228647.R
INFO 2025-04-24 12:59:22 ProcessExecutor [1] "Checking if R is installed"
[Thu Apr 24 12:59:22 EDT 2025] CollectMultipleMetrics --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/summary_alignment_stats_test.sam --OUTPUT /tmp/alignmentMetrics16844148412515903306 --METRIC_ACCUMULATION_LEVEL ALL_READS --PROGRAM CollectAlignmentSummaryMetrics --PROGRAM CollectInsertSizeMetrics --EXTRA_ARGUMENT QualityScoreDistribution::--HISTOGRAM_WIDTH 58 --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/summary_alignment_stats_test.fasta --ASSUME_SORTED true --STOP_AFTER 0 --INCLUDE_UNPAIRED false --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 12:59:22 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 12:59:22 EDT 2025] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
INFO 2025-04-24 12:59:22 RExecutor Executing R script via command: Rscript /tmp/script179648052931447763.R
INFO 2025-04-24 12:59:22 ProcessExecutor [1] "Checking if R is installed"
[Thu Apr 24 12:59:22 EDT 2025] CollectMultipleMetrics --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/summary_alignment_stats_test.sam --OUTPUT /tmp/alignmentMetrics2536645535723278474 --METRIC_ACCUMULATION_LEVEL ALL_READS --PROGRAM CollectAlignmentSummaryMetrics --PROGRAM CollectInsertSizeMetrics --EXTRA_ARGUMENT CollectInsertSizeMetrics::--BLAH 58 --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/summary_alignment_stats_test.fasta --ASSUME_SORTED true --STOP_AFTER 0 --INCLUDE_UNPAIRED false --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 12:59:22 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 12:59:22 EDT 2025] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
INFO 2025-04-24 12:59:22 RExecutor Executing R script via command: Rscript /tmp/script2961775623830575732.R
INFO 2025-04-24 12:59:22 ProcessExecutor [1] "Checking if R is installed"
[Thu Apr 24 12:59:22 EDT 2025] CollectMultipleMetrics --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/summary_alignment_stats_test.sam --OUTPUT /tmp/alignmentMetrics6570312114575456056 --METRIC_ACCUMULATION_LEVEL ALL_READS --PROGRAM CollectAlignmentSummaryMetrics --PROGRAM CollectInsertSizeMetrics --EXTRA_ARGUMENT CollectInsertSizeMetrics:HISTOGRAM_WIDTH 58 --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/summary_alignment_stats_test.fasta --ASSUME_SORTED true --STOP_AFTER 0 --INCLUDE_UNPAIRED false --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 12:59:22 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 12:59:22 EDT 2025] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
INFO 2025-04-24 12:59:22 RExecutor Executing R script via command: Rscript /tmp/script12157544025575019626.R
INFO 2025-04-24 12:59:22 ProcessExecutor [1] "Checking if R is installed"
[Thu Apr 24 12:59:22 EDT 2025] CollectMultipleMetrics --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/summary_alignment_stats_test.sam --OUTPUT /tmp/alignmentMetrics7779071328076180202 --METRIC_ACCUMULATION_LEVEL ALL_READS --PROGRAM CollectAlignmentSummaryMetrics --PROGRAM CollectInsertSizeMetrics --EXTRA_ARGUMENT CollectInsertSizeMetrics::--HISTOGRAM_WIDTH 5a8 --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/summary_alignment_stats_test.fasta --ASSUME_SORTED true --STOP_AFTER 0 --INCLUDE_UNPAIRED false --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 12:59:22 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 12:59:22 EDT 2025] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
INFO 2025-04-24 12:59:22 RExecutor Executing R script via command: Rscript /tmp/script14898783391644757405.R
INFO 2025-04-24 12:59:22 ProcessExecutor [1] "Checking if R is installed"
[Thu Apr 24 12:59:22 EDT 2025] CollectMultipleMetrics --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/summary_alignment_stats_test.sam --OUTPUT /tmp/alignmentMetrics1983820832621001631 --METRIC_ACCUMULATION_LEVEL ALL_READS --PROGRAM CollectAlignmentSummaryMetrics --PROGRAM CollectInsertSizeMetrics --EXTRA_ARGUMENT CollectInsertSizeMetrics::--HISTOGRAM_WIDTH --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/summary_alignment_stats_test.fasta --ASSUME_SORTED true --STOP_AFTER 0 --INCLUDE_UNPAIRED false --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 12:59:22 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 12:59:22 EDT 2025] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
INFO 2025-04-24 12:59:22 RExecutor Executing R script via command: Rscript /tmp/script18160586331684547589.R
INFO 2025-04-24 12:59:22 ProcessExecutor [1] "Checking if R is installed"
[Thu Apr 24 12:59:22 EDT 2025] CollectMultipleMetrics --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/summary_alignment_stats_test.sam --OUTPUT /tmp/alignmentMetrics11387068263250442413 --METRIC_ACCUMULATION_LEVEL ALL_READS --PROGRAM CollectAlignmentSummaryMetrics --PROGRAM CollectInsertSizeMetrics --EXTRA_ARGUMENT CollectInsertSizeMetrics::--HISTOGRAM_WIDTH hello --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/summary_alignment_stats_test.fasta --ASSUME_SORTED true --STOP_AFTER 0 --INCLUDE_UNPAIRED false --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 12:59:22 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 12:59:22 EDT 2025] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
INFO 2025-04-24 12:59:23 RExecutor Executing R script via command: Rscript /tmp/script7880210742447832088.R
INFO 2025-04-24 12:59:23 ProcessExecutor [1] "Checking if R is installed"
[Thu Apr 24 12:59:23 EDT 2025] CollectMultipleMetrics --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/summary_alignment_stats_test.sam --OUTPUT /tmp/alignmentMetrics11785758253721832114 --METRIC_ACCUMULATION_LEVEL ALL_READS --PROGRAM CollectAlignmentSummaryMetrics --PROGRAM CollectInsertSizeMetrics --EXTRA_ARGUMENT CollectInsertSizeMetrics::--REFERENCE whyNot.fasta --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/summary_alignment_stats_test.fasta --ASSUME_SORTED true --STOP_AFTER 0 --INCLUDE_UNPAIRED false --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 12:59:23 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 12:59:23 EDT 2025] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
INFO 2025-04-24 12:59:23 RExecutor Executing R script via command: Rscript /tmp/script13561983196452861941.R
INFO 2025-04-24 12:59:23 ProcessExecutor [1] "Checking if R is installed"
[Thu Apr 24 12:59:23 EDT 2025] CollectMultipleMetrics --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/summary_alignment_stats_test.sam --OUTPUT /tmp/alignmentMetrics7820650847427108272 --METRIC_ACCUMULATION_LEVEL ALL_READS --PROGRAM CollectAlignmentSummaryMetrics --PROGRAM CollectInsertSizeMetrics --EXTRA_ARGUMENT CollectInsertSizeMetrics::--OUTPUT --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/summary_alignment_stats_test.fasta --ASSUME_SORTED true --STOP_AFTER 0 --INCLUDE_UNPAIRED false --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 12:59:23 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 12:59:23 EDT 2025] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
INFO 2025-04-24 12:59:23 RExecutor Executing R script via command: Rscript /tmp/script3407882119300591504.R
INFO 2025-04-24 12:59:23 ProcessExecutor [1] "Checking if R is installed"
[Thu Apr 24 12:59:23 EDT 2025] CollectMultipleMetrics --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/rna_seq_metrics.sam --OUTPUT /tmp/tmp.2568431160313978836.rna_metrics --METRIC_ACCUMULATION_LEVEL ALL_READS --PROGRAM CollectAlignmentSummaryMetrics --PROGRAM CollectBaseDistributionByCycle --PROGRAM CollectInsertSizeMetrics --PROGRAM MeanQualityByCycle --PROGRAM QualityScoreDistribution --PROGRAM RnaSeqMetrics --INTERVALS /mounts/lovelace/software/picard/picard/testdata/picard/sam/rna_seq_metrics.interval_list --REF_FLAT /mounts/lovelace/software/picard/picard/testdata/picard/sam/rna_seq_metrics.refflat --IGNORE_SEQUENCE chrM --ASSUME_SORTED true --STOP_AFTER 0 --INCLUDE_UNPAIRED false --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 12:59:23 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 12:59:23 CollectAlignmentSummaryMetrics Without a REFERENCE_SEQUENCE, metrics pertaining to mismatch rates will not be collected!
INFO 2025-04-24 12:59:23 CollectRnaSeqMetrics Loaded 1 genes.
INFO 2025-04-24 12:59:23 RExecutor Executing R script via command: Rscript /tmp/script1668991730732919347.R /tmp/tmp.2568431160313978836.rna_metrics.alignment_summary_metrics /tmp/tmp.2568431160313978836.rna_metrics.read_length_histogram.pdf rna_seq_metrics.sam
INFO 2025-04-24 12:59:23 ProcessExecutor null device
INFO 2025-04-24 12:59:23 ProcessExecutor 1
INFO 2025-04-24 12:59:23 RExecutor Executing R script via command: Rscript /tmp/script11607123375546312864.R /tmp/tmp.2568431160313978836.rna_metrics.base_distribution_by_cycle_metrics /tmp/tmp.2568431160313978836.rna_metrics.base_distribution_by_cycle.pdf rna_seq_metrics.sam
INFO 2025-04-24 12:59:23 ProcessExecutor null device
INFO 2025-04-24 12:59:23 ProcessExecutor 1
INFO 2025-04-24 12:59:23 RExecutor Executing R script via command: Rscript /tmp/script2498619115002927192.R /tmp/tmp.2568431160313978836.rna_metrics.insert_size_metrics /tmp/tmp.2568431160313978836.rna_metrics.insert_size_histogram.pdf rna_seq_metrics.sam
INFO 2025-04-24 12:59:24 ProcessExecutor null device
INFO 2025-04-24 12:59:24 ProcessExecutor 1
INFO 2025-04-24 12:59:24 RExecutor Executing R script via command: Rscript /tmp/script3806205827502879375.R /tmp/tmp.2568431160313978836.rna_metrics.quality_by_cycle_metrics /tmp/tmp.2568431160313978836.rna_metrics.quality_by_cycle.pdf rna_seq_metrics.sam
INFO 2025-04-24 12:59:24 ProcessExecutor null device
INFO 2025-04-24 12:59:24 ProcessExecutor 1
INFO 2025-04-24 12:59:24 RExecutor Executing R script via command: Rscript /tmp/script506901356386821664.R /tmp/tmp.2568431160313978836.rna_metrics.quality_distribution_metrics /tmp/tmp.2568431160313978836.rna_metrics.quality_distribution.pdf rna_seq_metrics.sam
INFO 2025-04-24 12:59:24 ProcessExecutor null device
INFO 2025-04-24 12:59:24 ProcessExecutor 1
[Thu Apr 24 12:59:24 EDT 2025] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1073741824