Mercurial > repos > devteam > picard1106
comparison test-data/picard_output_hs_transposed_summary_alignment_stats.html @ 49:2bfb9ce28275 draft
Uploaded
author | devteam |
---|---|
date | Mon, 17 Feb 2014 00:02:22 -0500 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
48:d8d22fa853d6 | 49:2bfb9ce28275 |
---|---|
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 |