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1 <style type="text/css">
2 tr.d0 td {background-color: oldlace; color: black;}
3 tr.d1 td {background-color: aliceblue; color: black;}
4 </style><?xml version="1.0" encoding="utf-8" ?>
5 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
6 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
7 <head>
8 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
9 <meta name="generator" content="Galaxy picard_wrapper tool output - see http://getgalaxy.org/" />
10 <title></title>
11 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
12 </head>
13 <body>
14 <div class="document">
15 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>
16 <tr><td><a href="tempSamHead.txt">tempSamHead.txt</a></td></tr>
17 <tr><td><a href="rgPicardHsMetrics.bait">rgPicardHsMetrics.bait</a></td></tr>
18 <tr><td><a href="CalculateHsMetrics.metrics.txt">CalculateHsMetrics.metrics.txt</a></td></tr>
19 </table><p/>
20 <b>Picard on line resources - maxrows=100</b><ul>
21 <li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li>
22 <li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/>
23 <b>Picard output (transposed to make it easier to see)</b><hr/>
24 <table cellpadding="3" >
25 <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>
26 <tr class="d1"><td>GENOME_SIZE</td><td>2040</td></tr>
27 <tr class="d0"><td>BAIT_TERRITORY</td><td>14601938</td></tr>
28 <tr class="d1"><td>TARGET_TERRITORY</td><td>14601938</td></tr>
29 <tr class="d0"><td>BAIT_DESIGN_EFFICIENCY</td><td>1</td></tr>
30 <tr class="d1"><td>TOTAL_READS</td><td>18</td></tr>
31 <tr class="d0"><td>PF_READS</td><td>16</td></tr>
32 <tr class="d1"><td>PF_UNIQUE_READS</td><td>16</td></tr>
33 <tr class="d0"><td>PCT_PF_READS</td><td>0.888889</td></tr>
34 <tr class="d1"><td>PCT_PF_UQ_READS</td><td>0.888889</td></tr>
35 <tr class="d0"><td>PF_UQ_READS_ALIGNED</td><td>10</td></tr>
36 <tr class="d1"><td>PCT_PF_UQ_READS_ALIGNED</td><td>0.625</td></tr>
37 <tr class="d0"><td>PF_UQ_BASES_ALIGNED</td><td>1010</td></tr>
38 <tr class="d1"><td>ON_BAIT_BASES</td><td>0</td></tr>
39 <tr class="d0"><td>NEAR_BAIT_BASES</td><td>0</td></tr>
40 <tr class="d1"><td>OFF_BAIT_BASES</td><td>1010</td></tr>
41 <tr class="d0"><td>ON_TARGET_BASES</td><td>0</td></tr>
42 <tr class="d1"><td>PCT_SELECTED_BASES</td><td>0</td></tr>
43 <tr class="d0"><td>PCT_OFF_BAIT</td><td>1</td></tr>
44 <tr class="d1"><td>ON_BAIT_VS_SELECTED</td><td>?</td></tr>
45 <tr class="d0"><td>MEAN_BAIT_COVERAGE</td><td>0</td></tr>
46 <tr class="d1"><td>MEAN_TARGET_COVERAGE</td><td>?</td></tr>
47 <tr class="d0"><td>PCT_USABLE_BASES_ON_BAIT</td><td>0</td></tr>
48 <tr class="d1"><td>PCT_USABLE_BASES_ON_TARGET</td><td>0</td></tr>
49 <tr class="d0"><td>FOLD_ENRICHMENT</td><td>0</td></tr>
50 <tr class="d1"><td>ZERO_CVG_TARGETS_PCT</td><td>0.841776</td></tr>
51 <tr class="d0"><td>FOLD_80_BASE_PENALTY</td><td>?</td></tr>
52 <tr class="d1"><td>PCT_TARGET_BASES_2X</td><td>0</td></tr>
53 <tr class="d0"><td>PCT_TARGET_BASES_10X</td><td>0</td></tr>
54 <tr class="d1"><td>PCT_TARGET_BASES_20X</td><td>0</td></tr>
55 <tr class="d0"><td>PCT_TARGET_BASES_30X</td><td>0</td></tr>
56 <tr class="d1"><td>HS_LIBRARY_SIZE</td><td></td></tr>
57 <tr class="d0"><td>HS_PENALTY_10X</td><td>0</td></tr>
58 <tr class="d1"><td>HS_PENALTY_20X</td><td>0</td></tr>
59 <tr class="d0"><td>HS_PENALTY_30X
60 </td><td>0
61 </td></tr>
62 </table>
63 <b>Picard log</b><hr/>
64 <pre>## got 10 rows of header
65 ## 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:
66 [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
67 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8307873-8307942
68 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8309830-8309966
69 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8321581-8321736
70 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8328921-8329047
71 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8330342-8330469
72 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8331089-8331268
73 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8331692-8331978
74 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8365935-8366090
75 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8366606-8366726
76 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8379231-8379407
77 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8394536-8394660
78 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8426591-8426689
79 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8439724-8439837
80 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8450410-8450571
81 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8455465-8455675
82 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8460994-8461085
83 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8474118-8474378
84 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8475226-8475324
85 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8475761-8476349
86 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8482861-8482979
87 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8487241-8487268
88 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8489646-8489840
89 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8490753-8491059
90 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8494260-8494405
91 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8497300-8497434
92 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8507847-8508429
93 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8511276-8511546
94 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8513512-8513524
95 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8514924-8515035
96 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8516626-8516644
97 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8517344-8517353
98 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8518590-8518779
99 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8623316-8623458
100 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8626698-8626844
101 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8723779-8723843
102 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8307873-8307942
103 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8309830-8309966
104 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8321581-8321736
105 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8328921-8329047
106 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8330342-8330469
107 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8331089-8331268
108 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8331692-8331978
109 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8365935-8366090
110 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8366606-8366726
111 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8379231-8379407
112 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8394536-8394660
113 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8426591-8426689
114 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8439724-8439837
115 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8450410-8450571
116 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8455465-8455675
117 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8460994-8461085
118 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8474118-8474378
119 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8475226-8475324
120 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8475761-8476349
121 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8482861-8482979
122 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8487241-8487268
123 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8489646-8489840
124 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8490753-8491059
125 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8494260-8494405
126 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8497300-8497434
127 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8507847-8508429
128 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8511276-8511546
129 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8514924-8515035
130 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8518590-8518779
131 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8623316-8623458
132 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8626698-8626844
133 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8723779-8723843
134 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:16408986-16409647
135 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:16425552-16427522
136 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:16542527-16542763
137 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:16572980-16573083
138 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:16717794-16717995
139 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:16728357-16728483
140 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:16860643-16860646
141 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:125814448-125814568
142 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:125816060-125816263
143 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:125817221-125817625
144 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:125823198-125823404
145 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:125834519-125834807
146 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2019022-2019247
147 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2022951-2023081
148 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2029465-2029900
149 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2037228-2037484
150 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2044596-2044723
151 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2046671-2046845
152 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2048290-2048464
153 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2050815-2050986
154 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2060417-2060471
155 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2063211-2063342
156 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2063565-2063623
157 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2066228-2066329
158 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2067628-2067776
159 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2071831-2071995
160 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2073346-2073413
161 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2074085-2074196
162 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2076828-2077071
163 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2078499-2078613
164
165 <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>
166 generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html>
167