Galaxy tool CollectRnaSeqMetrics run at 26/02/2014 22:17:36
The following output files were created (click the filename to view/download a copy):
Picard on line resources
Picard output (transposed to make it easier to see)
| ## net.sf.picard.metrics.StringHeader |
| # net.sf.picard.analysis.CollectRnaSeqMetrics REF_FLAT=/home/dorine/galaxypicard/shed_tools/testtoolshed.g2.bx.psu.edu/repos/devteam/picard1106/c127b3314d53/picard1106/avenir/pourtest/refFlat.txt RIBOSOMAL_INTERVALS=null STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=CollectRnaSeqMetrics.pdf RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=/home/dorine/galaxypicard/shed_tools/testtoolshed.g2.bx.psu.edu/repos/devteam/picard1106/c127b3314d53/picard1106/avenir/pourtest/PICARD-in.sam OUTPUT=/home/dorine/galaxypicard/shed_tools/testtoolshed.g2.bx.psu.edu/repos/devteam/picard1106/c127b3314d53/picard1106/avenir/pourtest/masooortie_files/CollectRnaSeqMetrics.metrics.txt ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false |
| ## net.sf.picard.metrics.StringHeader |
| # Started on: Wed Feb 26 22:17:31 EST 2014 |
| ## METRICS CLASS net.sf.picard.analysis.RnaSeqMetrics |
| PF_BASES | 7321300 |
| PF_ALIGNED_BASES | 7319805 |
| RIBOSOMAL_BASES | |
| CODING_BASES | 0 |
| UTR_BASES | 0 |
| INTRONIC_BASES | 0 |
| INTERGENIC_BASES | 7319805 |
| IGNORED_READS | 0 |
| CORRECT_STRAND_READS | 0 |
| INCORRECT_STRAND_READS | 0 |
| PCT_RIBOSOMAL_BASES | |
| PCT_CODING_BASES | 0 |
| PCT_UTR_BASES | 0 |
| PCT_INTRONIC_BASES | 0 |
| PCT_INTERGENIC_BASES | 1 |
| PCT_MRNA_BASES | 0 |
| PCT_USABLE_BASES | 0 |
| PCT_CORRECT_STRAND_READS | 0 |
| MEDIAN_CV_COVERAGE | 0 |
| MEDIAN_5PRIME_BIAS | 0 |
| MEDIAN_3PRIME_BIAS | 0 |
| MEDIAN_5PRIME_TO_3PRIME_BIAS | 0 |
| SAMPLE | |
| LIBRARY | |
| READ_GROUP
|
|
Picard Tool Run Log
INFO:root:## executing java -Xmx3000m -Djava.io.tmpdir='/home/dorine/galaxypicard/galaxy-central/database/tmp' -jar /home/dorine/galaxypicard/shed_tools/testtoolshed.g2.bx.psu.edu/repos/devteam/picard1106/c127b3314d53/picard1106/avenir/pourtest/CollectRnaSeqMetrics.jar VALIDATION_STRINGENCY=LENIENT I=/home/dorine/galaxypicard/shed_tools/testtoolshed.g2.bx.psu.edu/repos/devteam/picard1106/c127b3314d53/picard1106/avenir/pourtest/PICARD-in.sam O=/home/dorine/galaxypicard/shed_tools/testtoolshed.g2.bx.psu.edu/repos/devteam/picard1106/c127b3314d53/picard1106/avenir/pourtest/masooortie_files/CollectRnaSeqMetrics.metrics.txt CHART_OUTPUT=CollectRnaSeqMetrics.pdf ASSUME_SORTED=true MINIMUM_LENGTH=500 REF_FLAT=/home/dorine/galaxypicard/shed_tools/testtoolshed.g2.bx.psu.edu/repos/devteam/picard1106/c127b3314d53/picard1106/avenir/pourtest/refFlat.txt STRAND_SPECIFICITY=NONE RIBOSOMAL_INTERVALS=null RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=ALL_READS returned status 0 and nothing on stderr
INFO:root:Unable to find expected pdf file /home/dorine/galaxypicard/shed_tools/testtoolshed.g2.bx.psu.edu/repos/devteam/picard1106/c127b3314d53/picard1106/avenir/pourtest/masooortie_files/CollectRnaSeqMetrics.pdf
The freely available
Picard software
generated all outputs reported here running as a
Galaxy tool