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Fix for FastqToSam MAX_Q usage detection.
author Daniel Blankenberg <dan@bx.psu.edu>
date Fri, 03 May 2013 17:13:01 -0400
parents 1cd7f3b42609
children
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Galaxy tool wrapper run picard_wrapper at 07/05/2011 00:15:30</b><br/><b>The following output files were created (click the filename to view/download a copy):</b><hr/><table>
<tr><td><a href="tempSamHead.txt">tempSamHead.txt</a></td></tr>
<tr><td><a href="rgPicardHsMetrics.bait">rgPicardHsMetrics.bait</a></td></tr>
<tr><td><a href="CalculateHsMetrics.metrics.txt">CalculateHsMetrics.metrics.txt</a></td></tr>
</table><p/>
<b>Picard on line resources - maxrows=100</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 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.directed.CalculateHsMetrics BAIT_INTERVALS=/udd/rerla/rgalaxy/database/job_working_directory/95/dataset_97_files/rgPicardHsMetrics.bait TARGET_INTERVALS=/udd/rerla/rgalaxy/database/job_working_directory/95/dataset_97_files/rgPicardHsMetrics.bait INPUT=/tmp/6728811.1.all.q/tmpCsP1vm/database/files/000/dataset_95.dat OUTPUT=/udd/rerla/rgalaxy/database/job_working_directory/95/dataset_97_files/CalculateHsMetrics.metrics.txt TMP_DIR=/tmp/6728811.1.all.q/tmpCsP1vm/database/tmp VALIDATION_STRINGENCY=LENIENT    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: Sat May 07 00:15:15 EDT 2011</td></tr><tr class="d0"><td>## METRICS CLASS	net.sf.picard.analysis.directed.HsMetrics</td></tr><tr class="d0"><td>BAIT_SET</td><td>rgPicardHsMetrics</td></tr>
<tr class="d1"><td>GENOME_SIZE</td><td>2040</td></tr>
<tr class="d0"><td>BAIT_TERRITORY</td><td>14601938</td></tr>
<tr class="d1"><td>TARGET_TERRITORY</td><td>14601938</td></tr>
<tr class="d0"><td>BAIT_DESIGN_EFFICIENCY</td><td>1</td></tr>
<tr class="d1"><td>TOTAL_READS</td><td>18</td></tr>
<tr class="d0"><td>PF_READS</td><td>16</td></tr>
<tr class="d1"><td>PF_UNIQUE_READS</td><td>16</td></tr>
<tr class="d0"><td>PCT_PF_READS</td><td>0.888889</td></tr>
<tr class="d1"><td>PCT_PF_UQ_READS</td><td>0.888889</td></tr>
<tr class="d0"><td>PF_UQ_READS_ALIGNED</td><td>10</td></tr>
<tr class="d1"><td>PCT_PF_UQ_READS_ALIGNED</td><td>0.625</td></tr>
<tr class="d0"><td>PF_UQ_BASES_ALIGNED</td><td>1010</td></tr>
<tr class="d1"><td>ON_BAIT_BASES</td><td>0</td></tr>
<tr class="d0"><td>NEAR_BAIT_BASES</td><td>0</td></tr>
<tr class="d1"><td>OFF_BAIT_BASES</td><td>1010</td></tr>
<tr class="d0"><td>ON_TARGET_BASES</td><td>0</td></tr>
<tr class="d1"><td>PCT_SELECTED_BASES</td><td>0</td></tr>
<tr class="d0"><td>PCT_OFF_BAIT</td><td>1</td></tr>
<tr class="d1"><td>ON_BAIT_VS_SELECTED</td><td>?</td></tr>
<tr class="d0"><td>MEAN_BAIT_COVERAGE</td><td>0</td></tr>
<tr class="d1"><td>MEAN_TARGET_COVERAGE</td><td>?</td></tr>
<tr class="d0"><td>PCT_USABLE_BASES_ON_BAIT</td><td>0</td></tr>
<tr class="d1"><td>PCT_USABLE_BASES_ON_TARGET</td><td>0</td></tr>
<tr class="d0"><td>FOLD_ENRICHMENT</td><td>0</td></tr>
<tr class="d1"><td>ZERO_CVG_TARGETS_PCT</td><td>0.841776</td></tr>
<tr class="d0"><td>FOLD_80_BASE_PENALTY</td><td>?</td></tr>
<tr class="d1"><td>PCT_TARGET_BASES_2X</td><td>0</td></tr>
<tr class="d0"><td>PCT_TARGET_BASES_10X</td><td>0</td></tr>
<tr class="d1"><td>PCT_TARGET_BASES_20X</td><td>0</td></tr>
<tr class="d0"><td>PCT_TARGET_BASES_30X</td><td>0</td></tr>
<tr class="d1"><td>HS_LIBRARY_SIZE</td><td></td></tr>
<tr class="d0"><td>HS_PENALTY_10X</td><td>0</td></tr>
<tr class="d1"><td>HS_PENALTY_20X</td><td>0</td></tr>
<tr class="d0"><td>HS_PENALTY_30X
</td><td>0
</td></tr>
</table>
<b>Picard log</b><hr/>
<pre>## got 10 rows of header
## executing java -Xmx8G -jar /udd/rerla/rgalaxy/tool-data/shared/jars/CalculateHsMetrics.jar VALIDATION_STRINGENCY=LENIENT BAIT_INTERVALS=/udd/rerla/rgalaxy/database/job_working_directory/95/dataset_97_files/rgPicardHsMetrics.bait TARGET_INTERVALS=/udd/rerla/rgalaxy/database/job_working_directory/95/dataset_97_files/rgPicardHsMetrics.bait INPUT=/tmp/6728811.1.all.q/tmpCsP1vm/database/files/000/dataset_95.dat OUTPUT=/udd/rerla/rgalaxy/database/job_working_directory/95/dataset_97_files/CalculateHsMetrics.metrics.txt TMP_DIR=/tmp/6728811.1.all.q/tmpCsP1vm/database/tmp returned status 0 and stderr: 
[Sat May 07 00:15:15 EDT 2011] net.sf.picard.analysis.directed.CalculateHsMetrics BAIT_INTERVALS=/udd/rerla/rgalaxy/database/job_working_directory/95/dataset_97_files/rgPicardHsMetrics.bait TARGET_INTERVALS=/udd/rerla/rgalaxy/database/job_working_directory/95/dataset_97_files/rgPicardHsMetrics.bait INPUT=/tmp/6728811.1.all.q/tmpCsP1vm/database/files/000/dataset_95.dat OUTPUT=/udd/rerla/rgalaxy/database/job_working_directory/95/dataset_97_files/CalculateHsMetrics.metrics.txt TMP_DIR=/tmp/6728811.1.all.q/tmpCsP1vm/database/tmp VALIDATION_STRINGENCY=LENIENT    VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8307873-8307942
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8309830-8309966
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8321581-8321736
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8328921-8329047
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8330342-8330469
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8331089-8331268
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8331692-8331978
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8365935-8366090
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8366606-8366726
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8379231-8379407
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8394536-8394660
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8426591-8426689
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8439724-8439837
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8450410-8450571
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8455465-8455675
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8460994-8461085
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8474118-8474378
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8475226-8475324
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8475761-8476349
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8482861-8482979
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8487241-8487268
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8489646-8489840
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8490753-8491059
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8494260-8494405
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8497300-8497434
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8507847-8508429
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8511276-8511546
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8513512-8513524
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8514924-8515035
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8516626-8516644
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8517344-8517353
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8518590-8518779
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8623316-8623458
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8626698-8626844
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8723779-8723843
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8307873-8307942
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8309830-8309966
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8321581-8321736
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8328921-8329047
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8330342-8330469
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8331089-8331268
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8331692-8331978
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8365935-8366090
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8366606-8366726
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8379231-8379407
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8394536-8394660
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8426591-8426689
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8439724-8439837
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8450410-8450571
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8455465-8455675
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8460994-8461085
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8474118-8474378
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8475226-8475324
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8475761-8476349
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8482861-8482979
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8487241-8487268
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8489646-8489840
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8490753-8491059
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8494260-8494405
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8497300-8497434
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8507847-8508429
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8511276-8511546
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8514924-8515035
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8518590-8518779
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8623316-8623458
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8626698-8626844
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8723779-8723843
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:16408986-16409647
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:16425552-16427522
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:16542527-16542763
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:16572980-16573083
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:16717794-16717995
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:16728357-16728483
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:16860643-16860646
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:125814448-125814568
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:125816060-125816263
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:125817221-125817625
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:125823198-125823404
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:125834519-125834807
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:2019022-2019247
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:2022951-2023081
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:2029465-2029900
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:2037228-2037484
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:2044596-2044723
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:2046671-2046845
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:2048290-2048464
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:2050815-2050986
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:2060417-2060471
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:2063211-2063342
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:2063565-2063623
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:2066228-2066329
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:2067628-2067776
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:2071831-2071995
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:2073346-2073413
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:2074085-2074196
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:2076828-2077071
WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:2078499-2078613

<b>## WARNING - 434559 log lines truncated - CalculateHsMetrics.log contains entire output</pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> 
generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html>