commit/galaxy-central: fubar: Grrrr. Must have index - trying hg19 to see if that pleases the buildbot on picard asmetrics
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/6690fe6f5e1c/ changeset: r5520:6690fe6f5e1c user: fubar date: 2011-05-09 17:07:01 summary: Grrrr. Must have index - trying hg19 to see if that pleases the buildbot on picard asmetrics affected #: 3 files (1.3 KB)
--- a/test-data/picard_output_AsMetrics_indexed_hg18_sorted_pair.html Mon May 09 10:57:14 2011 -0400 +++ b/test-data/picard_output_AsMetrics_indexed_hg18_sorted_pair.html Mon May 09 11:07:01 2011 -0400 @@ -1,35 +1,34 @@ <style type="text/css"> - tr.d0 td {background-color: oldlace; color: black;} - tr.d1 td {background-color: aliceblue; color: black;} - </style><?xml version="1.0" encoding="utf-8" ?> + tr.d0 td {background-color: oldlace; color: black;} + tr.d1 td {background-color: aliceblue; color: black;} + </style><?xml version="1.0" encoding="utf-8" ?><!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> -<meta name="generator" content="Galaxy rgPicardASMetrics.py tool output - see http://g2.trac.bx.psu.edu/" /> +<meta name="generator" content="Galaxy CollectAlignmentSummaryMetrics tool output - see http://getgalaxy.org/" /><title></title><link rel="stylesheet" href="/static/style/base.css" type="text/css" /></head><body><div class="document"> -<h3><a href="http://rgenetics.org">Rgenetics</a> tool rgPicardASMetrics.py run at 09/05/2011 10:53:44</h3><b>Your job produced the following output files.</b><hr/> -<table> -<tr><td><a href="AsMetricsIndexed.log">AsMetricsIndexed.log</a></td></tr> +Galaxy tool wrapper picard_wrapper at 09/05/2011 11:03:57</b><br/><b>The following output files were created (click the filename to view/download a copy):</b><hr/><table> +<tr><td><a href="CollectAlignmentSummaryMetrics.log">CollectAlignmentSummaryMetrics.log</a></td></tr></table><p/> -<b>No Picard output found - please consult the Picard log above for an explanation</b><b>Picard log</b><hr/> -<pre>[Mon May 09 10:53:44 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=false] INPUT=/export/tmp/tmpp-lP_s/database/files/000/dataset_4.dat OUTPUT=/share/shared/galaxy/database/job_working_directory/5/dataset_5_files/rgPicardASMetrics.out REFERENCE_SEQUENCE=/share/shared/data/genomes/hg18/hg18.fasta ASSUME_SORTED=true TMP_DIR=/tmp VALIDATION_STRINGENCY=LENIENT IS_BISULFITE_SEQUENCED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false -[Mon May 09 10:53:44 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics done. -Runtime.totalMemory()=9109504 -Exception in thread "main" net.sf.samtools.util.SequenceUtil$SequenceListsDifferException: Sequence dictionaries are not the same size (3, 45) - at net.sf.samtools.util.SequenceUtil.assertSequenceListsEqual(SequenceUtil.java:93) - at net.sf.samtools.util.SequenceUtil.assertSequenceDictionariesEqual(SequenceUtil.java:135) - at net.sf.picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:78) +<b>Picard log</b><hr/> +<pre>## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/shared/jars/CollectAlignmentSummaryMetrics.jar VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true ADAPTER_SEQUENCE= IS_BISULFITE_SEQUENCED=false MAX_INSERT_SIZE=100000 OUTPUT=/udd/rerla/galaxy-central/database/job_working_directory/5/dataset_5_files/CollectAlignmentSummaryMetrics.metrics.txt R=/udd/rerla/galaxy-central/database/job_working_directory/5/dataset_5_files/hg19.fasta_fake.fasta TMP_DIR=/tmp INPUT=/export/tmp/tmpBrCiH5/database/files/000/dataset_4.dat returned status 1 and stderr: +[Mon May 09 11:03:51 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=false] INPUT=/export/tmp/tmpBrCiH5/database/files/000/dataset_4.dat OUTPUT=/udd/rerla/galaxy-central/database/job_working_directory/5/dataset_5_files/CollectAlignmentSummaryMetrics.metrics.txt REFERENCE_SEQUENCE=/udd/rerla/galaxy-central/database/job_working_directory/5/dataset_5_files/hg19.fasta_fake.fasta ASSUME_SORTED=true TMP_DIR=/tmp VALIDATION_STRINGENCY=LENIENT IS_BISULFITE_SEQUENCED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +[Mon May 09 11:03:57 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics done. +Runtime.totalMemory()=912588800 +Exception in thread "main" net.sf.picard.PicardException: Requesting earlier reference sequence: 0 < 1 + at net.sf.picard.reference.ReferenceSequenceFileWalker.get(ReferenceSequenceFileWalker.java:78) + at net.sf.picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:115) at net.sf.picard.analysis.SinglePassSamProgram.doWork(SinglePassSamProgram.java:54) at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:157) at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:117) at net.sf.picard.analysis.CollectAlignmentSummaryMetrics.main(CollectAlignmentSummaryMetrics.java:106) + + </pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> -generated all outputs reported here, using this command line:<br/> -<pre>java -Xmx2g -jar /share/shared/galaxy/tool-data/shared/jars/CollectAlignmentSummaryMetrics.jar REFERENCE_SEQUENCE=/share/shared/data/genomes/hg18/hg18.fasta ASSUME_SORTED=true ADAPTER_SEQUENCE= IS_BISULFITE_SEQUENCED=false MAX_INSERT_SIZE=100000 INPUT=/export/tmp/tmpp-lP_s/database/files/000/dataset_4.dat OUTPUT=/share/shared/galaxy/database/job_working_directory/5/dataset_5_files/rgPicardASMetrics.out VALIDATION_STRINGENCY=LENIENT TMP_DIR=/tmp</pre> -</div></body></html> +generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html>
--- a/test-data/picard_output_alignment_summary_metrics.html Mon May 09 10:57:14 2011 -0400 +++ b/test-data/picard_output_alignment_summary_metrics.html Mon May 09 11:07:01 2011 -0400 @@ -1,56 +1,62 @@ <style type="text/css"> - tr.d0 td {background-color: oldlace; color: black;} - tr.d1 td {background-color: aliceblue; color: black;} - </style><?xml version="1.0" encoding="utf-8" ?> + tr.d0 td {background-color: oldlace; color: black;} + tr.d1 td {background-color: aliceblue; color: black;} + </style><?xml version="1.0" encoding="utf-8" ?><!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> -<meta name="generator" content="Galaxy rgPicardASMetrics.py tool output - see http://g2.trac.bx.psu.edu/" /> +<meta name="generator" content="Galaxy CollectAlignmentSummaryMetrics tool output - see http://getgalaxy.org/" /><title></title><link rel="stylesheet" href="/static/style/base.css" type="text/css" /></head><body><div class="document"> -<h3><a href="http://rgenetics.org">Rgenetics</a> tool rgPicardASMetrics.py run at 09/05/2011 10:53:32</h3><b>Your job produced the following output files.</b><hr/> -<table> -<tr><td><a href="rgPicardASMetrics.out">rgPicardASMetrics.out</a></td></tr> -<tr><td><a href="AsMetrics.log">AsMetrics.log</a></td></tr> +Galaxy tool wrapper picard_wrapper at 09/05/2011 11:03:41</b><br/><b>The following output files were created (click the filename to view/download a copy):</b><hr/><table> +<tr><td><a href="CollectAlignmentSummaryMetrics.log">CollectAlignmentSummaryMetrics.log</a></td></tr> +<tr><td><a href="CollectAlignmentSummaryMetrics.metrics.txt">CollectAlignmentSummaryMetrics.metrics.txt</a></td></tr></table><p/> -<b>Picard on line resources</b><ul> +<b>Picard on line resources:</b><ul><li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li><li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/> -<b>Picard output (transposed for readability)</b><hr/> +<b>Picard output (transposed to make it easier to see)</b><hr/><table cellpadding="3" > -<tr class="d0"><td>## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td># net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=false] INPUT=/export/tmp/tmpp-lP_s/database/files/000/dataset_2.dat OUTPUT=/share/shared/galaxy/database/job_working_directory/3/dataset_3_files/rgPicardASMetrics.out REFERENCE_SEQUENCE=/export/tmp/tmpp-lP_s/database/files/000/dataset_1.dat.fasta ASSUME_SORTED=true TMP_DIR=/tmp VALIDATION_STRINGENCY=LENIENT IS_BISULFITE_SEQUENCED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false</td></tr><tr class="d0"><td>## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td># Started on: Mon May 09 10:53:32 EDT 2011</td></tr><tr class="d0"><td>## METRICS CLASS net.sf.picard.analysis.AlignmentSummaryMetrics</td></tr><tr class="d1"><td>CATEGORY</td><td>FIRST_OF_PAIR</td></tr> -<tr class="d0"><td>TOTAL_READS</td><td>4</td></tr> -<tr class="d1"><td>PF_READS</td><td>4</td></tr> -<tr class="d0"><td>PCT_PF_READS</td><td>1</td></tr> -<tr class="d1"><td>PF_NOISE_READS</td><td>0</td></tr> -<tr class="d0"><td>PF_READS_ALIGNED</td><td>4</td></tr> -<tr class="d1"><td>PCT_PF_READS_ALIGNED</td><td>1</td></tr> -<tr class="d0"><td>PF_HQ_ALIGNED_READS</td><td>4</td></tr> -<tr class="d1"><td>PF_HQ_ALIGNED_BASES</td><td>404</td></tr> -<tr class="d0"><td>PF_HQ_ALIGNED_Q20_BASES</td><td>28</td></tr> -<tr class="d1"><td>PF_HQ_MEDIAN_MISMATCHES</td><td>78</td></tr> -<tr class="d0"><td>PF_HQ_ERROR_RATE</td><td>0.777228</td></tr> -<tr class="d1"><td>MEAN_READ_LENGTH</td><td>101</td></tr> -<tr class="d0"><td>READS_ALIGNED_IN_PAIRS</td><td>3</td></tr> -<tr class="d1"><td>PCT_READS_ALIGNED_IN_PAIRS</td><td>0.75</td></tr> -<tr class="d0"><td>BAD_CYCLES</td><td>63</td></tr> -<tr class="d1"><td>STRAND_BALANCE</td><td>0.25</td></tr> -<tr class="d0"><td>PCT_CHIMERAS</td><td>0</td></tr> -<tr class="d1"><td>PCT_ADAPTER +<tr class="d0"><td>## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td># net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=false] INPUT=/export/tmp/tmpBrCiH5/database/files/000/dataset_2.dat OUTPUT=/udd/rerla/galaxy-central/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetrics.metrics.txt REFERENCE_SEQUENCE=/udd/rerla/galaxy-central/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetricsDXFFCP.fasta_fake.fasta ASSUME_SORTED=true TMP_DIR=/tmp VALIDATION_STRINGENCY=LENIENT IS_BISULFITE_SEQUENCED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false</td></tr><tr class="d0"><td>## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td># Started on: Mon May 09 11:03:41 EDT 2011</td></tr><tr class="d0"><td>## METRICS CLASS net.sf.picard.analysis.AlignmentSummaryMetrics</td></tr><tr class="d0"><td>CATEGORY</td><td>FIRST_OF_PAIR</td></tr> +<tr class="d1"><td>TOTAL_READS</td><td>4</td></tr> +<tr class="d0"><td>PF_READS</td><td>4</td></tr> +<tr class="d1"><td>PCT_PF_READS</td><td>1</td></tr> +<tr class="d0"><td>PF_NOISE_READS</td><td>0</td></tr> +<tr class="d1"><td>PF_READS_ALIGNED</td><td>4</td></tr> +<tr class="d0"><td>PCT_PF_READS_ALIGNED</td><td>1</td></tr> +<tr class="d1"><td>PF_HQ_ALIGNED_READS</td><td>4</td></tr> +<tr class="d0"><td>PF_HQ_ALIGNED_BASES</td><td>404</td></tr> +<tr class="d1"><td>PF_HQ_ALIGNED_Q20_BASES</td><td>28</td></tr> +<tr class="d0"><td>PF_HQ_MEDIAN_MISMATCHES</td><td>78</td></tr> +<tr class="d1"><td>PF_HQ_ERROR_RATE</td><td>0.777228</td></tr> +<tr class="d0"><td>MEAN_READ_LENGTH</td><td>101</td></tr> +<tr class="d1"><td>READS_ALIGNED_IN_PAIRS</td><td>3</td></tr> +<tr class="d0"><td>PCT_READS_ALIGNED_IN_PAIRS</td><td>0.75</td></tr> +<tr class="d1"><td>BAD_CYCLES</td><td>63</td></tr> +<tr class="d0"><td>STRAND_BALANCE</td><td>0.25</td></tr> +<tr class="d1"><td>PCT_CHIMERAS</td><td>0</td></tr> +<tr class="d0"><td>PCT_ADAPTER </td><td>0 </td></tr></table><b>Picard log</b><hr/> -<pre>[Mon May 09 10:53:32 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=false] INPUT=/export/tmp/tmpp-lP_s/database/files/000/dataset_2.dat OUTPUT=/share/shared/galaxy/database/job_working_directory/3/dataset_3_files/rgPicardASMetrics.out REFERENCE_SEQUENCE=/export/tmp/tmpp-lP_s/database/files/000/dataset_1.dat.fasta ASSUME_SORTED=true TMP_DIR=/tmp VALIDATION_STRINGENCY=LENIENT IS_BISULFITE_SEQUENCED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false -WARNING 2011-05-09 10:53:32 SinglePassSamProgram File reports sort order 'queryname', assuming it's coordinate sorted anyway. -[Mon May 09 10:53:32 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics done. +<pre>## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/shared/jars/CreateSequenceDictionary.jar REFERENCE=/tmp/CollectAlignmentSummaryMetricsDXFFCP.fasta OUTPUT=/tmp/CollectAlignmentSummaryMetricsDXFFCP.dict URI=dataset_1.dat TRUNCATE_NAMES_AT_WHITESPACE=None returned status 0 and stderr: +[Mon May 09 11:03:40 EDT 2011] net.sf.picard.sam.CreateSequenceDictionary REFERENCE=/tmp/CollectAlignmentSummaryMetricsDXFFCP.fasta OUTPUT=/tmp/CollectAlignmentSummaryMetricsDXFFCP.dict URI=dataset_1.dat TRUNCATE_NAMES_AT_WHITESPACE=false NUM_SEQUENCES=2147483647 TMP_DIR=/tmp/rerla VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +[Mon May 09 11:03:40 EDT 2011] net.sf.picard.sam.CreateSequenceDictionary done. Runtime.totalMemory()=9109504 + + +## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/shared/jars/CollectAlignmentSummaryMetrics.jar VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true ADAPTER_SEQUENCE= IS_BISULFITE_SEQUENCED=false MAX_INSERT_SIZE=100000 OUTPUT=/udd/rerla/galaxy-central/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetrics.metrics.txt R=/udd/rerla/galaxy-central/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetricsDXFFCP.fasta_fake.fasta TMP_DIR=/tmp INPUT=/export/tmp/tmpBrCiH5/database/files/000/dataset_2.dat returned status 0 and stderr: +[Mon May 09 11:03:41 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=false] INPUT=/export/tmp/tmpBrCiH5/database/files/000/dataset_2.dat OUTPUT=/udd/rerla/galaxy-central/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetrics.metrics.txt REFERENCE_SEQUENCE=/udd/rerla/galaxy-central/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetricsDXFFCP.fasta_fake.fasta ASSUME_SORTED=true TMP_DIR=/tmp VALIDATION_STRINGENCY=LENIENT IS_BISULFITE_SEQUENCED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +WARNING 2011-05-09 11:03:41 SinglePassSamProgram File reports sort order 'queryname', assuming it's coordinate sorted anyway. +[Mon May 09 11:03:41 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics done. +Runtime.totalMemory()=9109504 + + </pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> -generated all outputs reported here, using this command line:<br/> -<pre>java -Xmx2g -jar /share/shared/galaxy/tool-data/shared/jars/CollectAlignmentSummaryMetrics.jar REFERENCE_SEQUENCE=/export/tmp/tmpp-lP_s/database/files/000/dataset_1.dat.fasta ASSUME_SORTED=true ADAPTER_SEQUENCE= IS_BISULFITE_SEQUENCED=false MAX_INSERT_SIZE=100000 INPUT=/export/tmp/tmpp-lP_s/database/files/000/dataset_2.dat OUTPUT=/share/shared/galaxy/database/job_working_directory/3/dataset_3_files/rgPicardASMetrics.out VALIDATION_STRINGENCY=LENIENT TMP_DIR=/tmp</pre> -</div></body></html> +generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html>
--- a/tools/picard/rgPicardASMetrics.xml Mon May 09 10:57:14 2011 -0400 +++ b/tools/picard/rgPicardASMetrics.xml Mon May 09 11:07:01 2011 -0400 @@ -70,7 +70,8 @@ <param name="adaptors" value="" /><param name="maxinsert" value="100000" /><param name="refGenomeSource" value="indexed" /> - <param name="input_file" value="picard_input_sorted_pair.sam" dbkey="hg18" /> + <param name="index" value="hg19" /> + <param name="input_file" value="picard_input_sorted_pair.sam" dbkey="hg19" /><output name="html_file" file="picard_output_AsMetrics_indexed_hg18_sorted_pair.html" ftype="html" lines_diff="50"/></test></tests>
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