Class picard.analysis.CollectInsertSizeMetricsTest

all > picard.analysis > CollectInsertSizeMetricsTest
tests
failures
ignored
1.996s
duration
100%
successful
Tests
Standard error
Tests

Test	Duration	Result
test	0.474s	passed
testHistogramWidthIsSetProperly	0.420s	passed
testMultipleOrientationsForHistogram	0.247s	passed
testPercentCharInPdfFilename	0.439s	passed
testWidthOfMetrics	0.416s	passed
Standard error

INFO	2025-04-24 12:59:17	RExecutor	Executing R script via command: Rscript /tmp/script12501205425176229029.R
INFO	2025-04-24 12:59:17	ProcessExecutor	[1] "Checking if R is installed"
[Thu Apr 24 12:59:17 EDT 2025] CollectInsertSizeMetrics --Histogram_FILE /tmp/test9233449655464315520.pdf --METRIC_ACCUMULATION_LEVEL ALL_READS --METRIC_ACCUMULATION_LEVEL SAMPLE --METRIC_ACCUMULATION_LEVEL READ_GROUP --METRIC_ACCUMULATION_LEVEL LIBRARY --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/insert_size_metrics_test.sam --OUTPUT /tmp/test15251464257504551552.insert_size_metrics --DEVIATIONS 10.0 --MINIMUM_PCT 0.05 --INCLUDE_DUPLICATES false --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 12:59:17 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/script7474184215593966059.R /tmp/test15251464257504551552.insert_size_metrics /tmp/test9233449655464315520.pdf insert_size_metrics_test.sam
INFO	2025-04-24 12:59:17	ProcessExecutor	null device 
INFO	2025-04-24 12:59:17	ProcessExecutor	          1 
[Thu Apr 24 12:59:17 EDT 2025] picard.analysis.CollectInsertSizeMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
INFO	2025-04-24 12:59:17	RExecutor	Executing R script via command: Rscript /tmp/script10891323211066597393.R
INFO	2025-04-24 12:59:18	ProcessExecutor	[1] "Checking if R is installed"
[Thu Apr 24 12:59:18 EDT 2025] CollectInsertSizeMetrics --Histogram_FILE /tmp/test2395958686069638777.pdf --METRIC_ACCUMULATION_LEVEL READ_GROUP --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/insert_size_metrics_test.sam --OUTPUT /tmp/test5790634952512321541.insert_size_metrics --DEVIATIONS 10.0 --MINIMUM_PCT 0.05 --INCLUDE_DUPLICATES false --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 12:59:18 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 12:59:18	RExecutor	Executing R script via command: Rscript /tmp/script9478224035480324022.R /tmp/test5790634952512321541.insert_size_metrics /tmp/test2395958686069638777.pdf insert_size_metrics_test.sam
INFO	2025-04-24 12:59:18	ProcessExecutor	null device 
INFO	2025-04-24 12:59:18	ProcessExecutor	          1 
[Thu Apr 24 12:59:18 EDT 2025] picard.analysis.CollectInsertSizeMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
INFO	2025-04-24 12:59:18	RExecutor	Executing R script via command: Rscript /tmp/script6916687626468392772.R /mounts/lovelace/software/picard/picard/testdata/picard/analysis/directed/CollectInsertSizeMetrics/multiple_orientation.sam.insert_size_metrics /tmp/test8368820972106123513.pdf Flags of Chad and Romania
INFO	2025-04-24 12:59:18	ProcessExecutor	null device 
INFO	2025-04-24 12:59:18	ProcessExecutor	          1 
INFO	2025-04-24 12:59:18	RExecutor	Executing R script via command: Rscript /tmp/script8137331995758681502.R
INFO	2025-04-24 12:59:18	ProcessExecutor	[1] "Checking if R is installed"
[Thu Apr 24 12:59:18 EDT 2025] CollectInsertSizeMetrics --Histogram_FILE /tmp/test_%_char10335306583216209467.pdf --METRIC_ACCUMULATION_LEVEL ALL_READS --METRIC_ACCUMULATION_LEVEL SAMPLE --METRIC_ACCUMULATION_LEVEL READ_GROUP --METRIC_ACCUMULATION_LEVEL LIBRARY --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/insert_size_metrics_test.sam --OUTPUT /tmp/test_%_char753808009473440728.insert_size_metrics --DEVIATIONS 10.0 --MINIMUM_PCT 0.05 --INCLUDE_DUPLICATES false --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 12:59:18 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 12:59:18	RExecutor	Executing R script via command: Rscript /tmp/script3608761292629861272.R /tmp/test_%_char753808009473440728.insert_size_metrics /tmp/test_%%_char10335306583216209467.pdf insert_size_metrics_test.sam
INFO	2025-04-24 12:59:19	ProcessExecutor	null device 
INFO	2025-04-24 12:59:19	ProcessExecutor	          1 
[Thu Apr 24 12:59:19 EDT 2025] picard.analysis.CollectInsertSizeMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
INFO	2025-04-24 12:59:19	RExecutor	Executing R script via command: Rscript /tmp/script2937801836082293576.R
INFO	2025-04-24 12:59:19	ProcessExecutor	[1] "Checking if R is installed"
[Thu Apr 24 12:59:19 EDT 2025] CollectInsertSizeMetrics --Histogram_FILE /tmp/test7331870703932771590.pdf --INPUT /tmp/CollectInsertSizeMetrics2174728236017808199.bam --OUTPUT /tmp/test18331378630970140011.insert_size_metrics --DEVIATIONS 10.0 --MINIMUM_PCT 0.05 --METRIC_ACCUMULATION_LEVEL ALL_READS --INCLUDE_DUPLICATES false --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 12:59:19 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/script17548146858808434922.R /tmp/test18331378630970140011.insert_size_metrics /tmp/test7331870703932771590.pdf CollectInsertSizeMetrics2174728236017808199.bam
INFO	2025-04-24 12:59:19	ProcessExecutor	null device 
INFO	2025-04-24 12:59:19	ProcessExecutor	          1 
[Thu Apr 24 12:59:19 EDT 2025] picard.analysis.CollectInsertSizeMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824