Class picard.analysis.CollectRnaSeqMetricsTest

all > picard.analysis > CollectRnaSeqMetricsTest
9

tests
0

failures
0

ignored
0.113s

duration
100%

successful

Tests

Test Duration Result
testBasic 0.014s passed
testBiasEndBiasAdjust[0](25, 0.0, 0.0, 0.0) 0.018s passed
testBiasEndBiasAdjust[1](50, 1.543624, 0.0, 0.0) 0.016s passed
testBiasEndBiasAdjust[2](100, 2.449664, 1.677852, 0.684932) 0.013s passed
testMultiLevel 0.012s passed
testNoIntevalsNoFragPercentage[0](null) 0.008s passed
testNoIntevalsNoFragPercentage[1](/tmp/tmp.rRna.7799416925500386212.interval_list) 0.011s passed
testPctRibosomalBases 0.010s passed
testTranscriptionStrandMetrics 0.011s passed

Standard error

[Thu Apr 24 12:59:25 EDT 2025] CollectRnaSeqMetrics --REF_FLAT /tmp/tmp.1547829341521615958.refFlat --RIBOSOMAL_INTERVALS /tmp/tmp.rRna.14222407913459183687.interval_list --STRAND_SPECIFICITY SECOND_READ_TRANSCRIPTION_STRAND --IGNORE_SEQUENCE chrM --INPUT /tmp/tmp.collectRnaSeqMetrics.17904853330600749306.sam --OUTPUT /tmp/tmp.9924887386372561431.rna_metrics --MINIMUM_LENGTH 500 --RRNA_FRAGMENT_PERCENTAGE 0.8 --METRIC_ACCUMULATION_LEVEL ALL_READS --END_BIAS_BASES 100 --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 12:59:25 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 12:59:25	CollectRnaSeqMetrics	Loaded 1 genes.
[Thu Apr 24 12:59:25 EDT 2025] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 12:59:25 EDT 2025] CollectRnaSeqMetrics --REF_FLAT /tmp/tmp.7405670453564483520.refFlat --STRAND_SPECIFICITY NONE --END_BIAS_BASES 25 --INPUT /tmp/tmp.collectRnaSeqMetrics.13565451748528013058.sam --OUTPUT /tmp/tmp.16491538782989003731.rna_metrics --MINIMUM_LENGTH 500 --RRNA_FRAGMENT_PERCENTAGE 0.8 --METRIC_ACCUMULATION_LEVEL ALL_READS --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 12:59:25 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 12:59:25	CollectRnaSeqMetrics	Loaded 1 genes.
[Thu Apr 24 12:59:25 EDT 2025] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 12:59:25 EDT 2025] CollectRnaSeqMetrics --REF_FLAT /tmp/tmp.4173743462469365661.refFlat --STRAND_SPECIFICITY NONE --END_BIAS_BASES 50 --INPUT /tmp/tmp.collectRnaSeqMetrics.13072967077315139071.sam --OUTPUT /tmp/tmp.17100443787753871054.rna_metrics --MINIMUM_LENGTH 500 --RRNA_FRAGMENT_PERCENTAGE 0.8 --METRIC_ACCUMULATION_LEVEL ALL_READS --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 12:59:25 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 12:59:25	CollectRnaSeqMetrics	Loaded 1 genes.
[Thu Apr 24 12:59:25 EDT 2025] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 12:59:25 EDT 2025] CollectRnaSeqMetrics --REF_FLAT /tmp/tmp.16588699364479914372.refFlat --STRAND_SPECIFICITY NONE --END_BIAS_BASES 100 --INPUT /tmp/tmp.collectRnaSeqMetrics.10723920229774756712.sam --OUTPUT /tmp/tmp.1698774409288820470.rna_metrics --MINIMUM_LENGTH 500 --RRNA_FRAGMENT_PERCENTAGE 0.8 --METRIC_ACCUMULATION_LEVEL ALL_READS --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 12:59:25 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 12:59:25	CollectRnaSeqMetrics	Loaded 1 genes.
[Thu Apr 24 12:59:25 EDT 2025] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 12:59:25 EDT 2025] CollectRnaSeqMetrics --REF_FLAT /tmp/tmp.12482138103536074163.refFlat --RIBOSOMAL_INTERVALS /tmp/tmp.rRna.7459844020945988821.interval_list --STRAND_SPECIFICITY SECOND_READ_TRANSCRIPTION_STRAND --IGNORE_SEQUENCE chrM --METRIC_ACCUMULATION_LEVEL SAMPLE --METRIC_ACCUMULATION_LEVEL LIBRARY --INPUT /tmp/tmp.collectRnaSeqMetrics.13086540833283609959.sam --OUTPUT /tmp/tmp.11373048901101701492.rna_metrics --MINIMUM_LENGTH 500 --RRNA_FRAGMENT_PERCENTAGE 0.8 --END_BIAS_BASES 100 --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 12:59:25 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 12:59:25	CollectRnaSeqMetrics	Loaded 1 genes.
[Thu Apr 24 12:59:25 EDT 2025] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 12:59:25 EDT 2025] CollectRnaSeqMetrics --REF_FLAT /tmp/tmp.12442106745030550381.refFlat --RIBOSOMAL_INTERVALS /tmp/tmp.rRna.7799416925500386212.interval_list --STRAND_SPECIFICITY SECOND_READ_TRANSCRIPTION_STRAND --IGNORE_SEQUENCE chrM --RRNA_FRAGMENT_PERCENTAGE 0.0 --INPUT /tmp/tmp.collectRnaSeqMetrics.2493815455657745494.sam --OUTPUT /tmp/tmp.962406479260103736.rna_metrics --MINIMUM_LENGTH 500 --METRIC_ACCUMULATION_LEVEL ALL_READS --END_BIAS_BASES 100 --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 12:59:25 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 12:59:25	CollectRnaSeqMetrics	Loaded 1 genes.
WARNING	2025-04-24 12:59:25	CollectRnaSeqMetrics	The RIBOSOMAL_INTERVALS file, /tmp/tmp.rRna.7799416925500386212.interval_list does not contain intervals
[Thu Apr 24 12:59:25 EDT 2025] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 12:59:25 EDT 2025] CollectRnaSeqMetrics --REF_FLAT /tmp/tmp.12567225963472699465.refFlat --RIBOSOMAL_INTERVALS /tmp/tmp.rRna.17257318901582895927.interval_list --STRAND_SPECIFICITY SECOND_READ_TRANSCRIPTION_STRAND --IGNORE_SEQUENCE chrM --INPUT /tmp/tmp.collectRnaSeqMetrics.1621298536403914184.sam --OUTPUT /tmp/tmp.10420237753069945565.rna_metrics --MINIMUM_LENGTH 500 --RRNA_FRAGMENT_PERCENTAGE 0.8 --METRIC_ACCUMULATION_LEVEL ALL_READS --END_BIAS_BASES 100 --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 12:59:25 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 12:59:25	CollectRnaSeqMetrics	Loaded 1 genes.
[Thu Apr 24 12:59:25 EDT 2025] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 12:59:25 EDT 2025] CollectRnaSeqMetrics --REF_FLAT /tmp/tmp.2178724748341989575.refFlat --RIBOSOMAL_INTERVALS /tmp/tmp.rRna.14720010798636059980.interval_list --STRAND_SPECIFICITY SECOND_READ_TRANSCRIPTION_STRAND --IGNORE_SEQUENCE chrM --INPUT /tmp/tmp.collectRnaSeqMetrics.8856585254475044579.sam --OUTPUT /tmp/tmp.17772652075702726389.rna_metrics --MINIMUM_LENGTH 500 --RRNA_FRAGMENT_PERCENTAGE 0.8 --METRIC_ACCUMULATION_LEVEL ALL_READS --END_BIAS_BASES 100 --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 12:59:25 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 12:59:25	CollectRnaSeqMetrics	Loaded 1 genes.
[Thu Apr 24 12:59:25 EDT 2025] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824