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/test-data/picard_output_markdups_sortedpairsam.html

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 15Galaxy tool MarkDuplicates run at 12/05/2011 14:34:29</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="MarkDuplicates.log">MarkDuplicates.log</a></td></tr>
 17<tr><td><a href="MarkDuplicates.metrics.txt">MarkDuplicates.metrics.txt</a></td></tr>
 18</table><p/>
 19<b>Picard on line resources</b><ul>
 20<li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li>
 21<li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/>
 22<b>Picard output (transposed to make it easier to see)</b><hr/>
 23<table cellpadding="3" >
 24<tr class="d0"><td colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># net.sf.picard.sam.MarkDuplicates INPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1097.dat OUTPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1098.dat METRICS_FILE=/udd/rerla/galaxy-central/database/job_working_directory/1032/dataset_1099_files/MarkDuplicates.metrics.txt REMOVE_DUPLICATES=true ASSUME_SORTED=true READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VALIDATION_STRINGENCY=LENIENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 TMP_DIR=/tmp/rerla 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 colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># Started on: Thu May 12 14:34:28 EDT 2011</td></tr><tr class="d0"><td colspan="2">## METRICS CLASS	net.sf.picard.sam.DuplicationMetrics</td></tr><tr class="d0"><td>LIBRARY</td><td>&nbsp;</td></tr>
 25<tr class="d1"><td>UNPAIRED_READS_EXAMINED</td><td>1&nbsp;</td></tr>
 26<tr class="d0"><td>READ_PAIRS_EXAMINED</td><td>3&nbsp;</td></tr>
 27<tr class="d1"><td>UNMAPPED_READS</td><td>1&nbsp;</td></tr>
 28<tr class="d0"><td>UNPAIRED_READ_DUPLICATES</td><td>1&nbsp;</td></tr>
 29<tr class="d1"><td>READ_PAIR_DUPLICATES</td><td>1&nbsp;</td></tr>
 30<tr class="d0"><td>READ_PAIR_OPTICAL_DUPLICATES</td><td>0&nbsp;</td></tr>
 31<tr class="d1"><td>PERCENT_DUPLICATION</td><td>0.428571&nbsp;</td></tr>
 32<tr class="d0"><td>ESTIMATED_LIBRARY_SIZE
 33</td><td>3
 34&nbsp;</td></tr>
 35<tr class="d0"><td colspan="2">## HISTOGRAM	java.lang.Double</td></tr><tr class="d0"><td colspan="2">BIN	VALUE</td></tr>
 36<tr class="d1"><td colspan="2">1.0	0.948181</td></tr>
 37<tr class="d0"><td colspan="2">2.0	1.296997</td></tr>
 38<tr class="d1"><td colspan="2">3.0	1.425319</td></tr>
 39<tr class="d0"><td colspan="2">4.0	1.472527</td></tr>
 40<tr class="d1"><td colspan="2">5.0	1.489893</td></tr>
 41<tr class="d0"><td colspan="2">6.0	1.496282</td></tr>
 42<tr class="d1"><td colspan="2">7.0	1.498632</td></tr>
 43<tr class="d0"><td colspan="2">8.0	1.499497</td></tr>
 44<tr class="d1"><td colspan="2">9.0	1.499815</td></tr>
 45<tr class="d0"><td colspan="2">10.0	1.499932</td></tr>
 46<tr class="d1"><td colspan="2">11.0	1.499975</td></tr>
 47<tr class="d0"><td colspan="2">12.0	1.499991</td></tr>
 48<tr class="d1"><td colspan="2">13.0	1.499997</td></tr>
 49<tr class="d0"><td colspan="2">14.0	1.499999</td></tr>
 50<tr class="d1"><td colspan="2">15.0	1.5</td></tr>
 51<tr class="d0"><td colspan="2">16.0	1.5</td></tr>
 52<tr class="d1"><td colspan="2">17.0	1.5</td></tr>
 53<tr class="d0"><td colspan="2">18.0	1.5</td></tr>
 54<tr class="d1"><td colspan="2">19.0	1.5</td></tr>
 55<tr class="d0"><td colspan="2">20.0	1.5</td></tr>
 56<tr class="d1"><td colspan="2">21.0	1.5</td></tr>
 57<tr class="d0"><td colspan="2">22.0	1.5</td></tr>
 58<tr class="d1"><td colspan="2">23.0	1.5</td></tr>
 59<tr class="d0"><td colspan="2">24.0	1.5</td></tr>
 60<tr class="d1"><td colspan="2">25.0	1.5</td></tr>
 61<tr class="d0"><td colspan="2">26.0	1.5</td></tr>
 62<tr class="d1"><td colspan="2">27.0	1.5</td></tr>
 63<tr class="d0"><td colspan="2">28.0	1.5</td></tr>
 64<tr class="d1"><td colspan="2">29.0	1.5</td></tr>
 65<tr class="d0"><td colspan="2">30.0	1.5</td></tr>
 66<tr class="d1"><td colspan="2">31.0	1.5</td></tr>
 67<tr class="d0"><td colspan="2">32.0	1.5</td></tr>
 68<tr class="d1"><td colspan="2">33.0	1.5</td></tr>
 69<tr class="d0"><td colspan="2">34.0	1.5</td></tr>
 70<tr class="d1"><td colspan="2">35.0	1.5</td></tr>
 71<tr class="d0"><td colspan="2">36.0	1.5</td></tr>
 72<tr class="d1"><td colspan="2">37.0	1.5</td></tr>
 73<tr class="d0"><td colspan="2">38.0	1.5</td></tr>
 74<tr class="d1"><td colspan="2">39.0	1.5</td></tr>
 75<tr class="d0"><td colspan="2">40.0	1.5</td></tr>
 76<tr class="d1"><td colspan="2">41.0	1.5</td></tr>
 77<tr class="d0"><td colspan="2">42.0	1.5</td></tr>
 78<tr class="d1"><td colspan="2">43.0	1.5</td></tr>
 79<tr class="d0"><td colspan="2">44.0	1.5</td></tr>
 80<tr class="d1"><td colspan="2">45.0	1.5</td></tr>
 81<tr class="d0"><td colspan="2">46.0	1.5</td></tr>
 82<tr class="d1"><td colspan="2">47.0	1.5</td></tr>
 83<tr class="d0"><td colspan="2">48.0	1.5</td></tr>
 84<tr class="d1"><td colspan="2">49.0	1.5</td></tr>
 85<tr class="d0"><td colspan="2">50.0	1.5</td></tr>
 86<tr class="d1"><td colspan="2">51.0	1.5</td></tr>
 87<tr class="d0"><td colspan="2">52.0	1.5</td></tr>
 88<tr class="d1"><td colspan="2">53.0	1.5</td></tr>
 89<tr class="d0"><td colspan="2">54.0	1.5</td></tr>
 90<tr class="d1"><td colspan="2">55.0	1.5</td></tr>
 91<tr class="d0"><td colspan="2">56.0	1.5</td></tr>
 92<tr class="d1"><td colspan="2">57.0	1.5</td></tr>
 93<tr class="d0"><td colspan="2">58.0	1.5</td></tr>
 94<tr class="d1"><td colspan="2">59.0	1.5</td></tr>
 95<tr class="d0"><td colspan="2">60.0	1.5</td></tr>
 96<tr class="d1"><td colspan="2">61.0	1.5</td></tr>
 97<tr class="d0"><td colspan="2">62.0	1.5</td></tr>
 98<tr class="d1"><td colspan="2">63.0	1.5</td></tr>
 99<tr class="d0"><td colspan="2">64.0	1.5</td></tr>
100<tr class="d1"><td colspan="2">65.0	1.5</td></tr>
101<tr class="d0"><td colspan="2">66.0	1.5</td></tr>
102<tr class="d1"><td colspan="2">67.0	1.5</td></tr>
103<tr class="d0"><td colspan="2">68.0	1.5</td></tr>
104<tr class="d1"><td colspan="2">69.0	1.5</td></tr>
105<tr class="d0"><td colspan="2">70.0	1.5</td></tr>
106<tr class="d1"><td colspan="2">71.0	1.5</td></tr>
107<tr class="d0"><td colspan="2">72.0	1.5</td></tr>
108<tr class="d1"><td colspan="2">73.0	1.5</td></tr>
109<tr class="d0"><td colspan="2">74.0	1.5</td></tr>
110<tr class="d1"><td colspan="2">75.0	1.5</td></tr>
111<tr class="d0"><td colspan="2">76.0	1.5</td></tr>
112<tr class="d1"><td colspan="2">77.0	1.5</td></tr>
113<tr class="d0"><td colspan="2">78.0	1.5</td></tr>
114<tr class="d1"><td colspan="2">79.0	1.5</td></tr>
115<tr class="d0"><td colspan="2">80.0	1.5</td></tr>
116<tr class="d1"><td colspan="2">81.0	1.5</td></tr>
117<tr class="d0"><td colspan="2">82.0	1.5</td></tr>
118<tr class="d1"><td colspan="2">83.0	1.5</td></tr>
119<tr class="d0"><td colspan="2">84.0	1.5</td></tr>
120<tr class="d1"><td colspan="2">85.0	1.5</td></tr>
121<tr class="d0"><td colspan="2">86.0	1.5</td></tr>
122<tr class="d1"><td colspan="2">87.0	1.5</td></tr>
123<tr class="d0"><td colspan="2">88.0	1.5</td></tr>
124<tr class="d1"><td colspan="2">89.0	1.5</td></tr>
125<tr class="d0"><td colspan="2">90.0	1.5</td></tr>
126<tr class="d1"><td colspan="2">91.0	1.5</td></tr>
127<tr class="d0"><td colspan="2">92.0	1.5</td></tr>
128<tr class="d1"><td colspan="2">93.0	1.5</td></tr>
129<tr class="d0"><td colspan="2">94.0	1.5</td></tr>
130<tr class="d1"><td colspan="2">95.0	1.5</td></tr>
131<tr class="d0"><td colspan="2">96.0	1.5</td></tr>
132<tr class="d1"><td colspan="2">97.0	1.5</td></tr>
133<tr class="d0"><td colspan="2">98.0	1.5</td></tr>
134<tr class="d1"><td colspan="2">99.0	1.5</td></tr>
135</table>
136<b>Picard Tool Run Log</b><hr/>
137<pre>Thu, 12 May 2011 14:34:29 INFO
138 ## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/shared/jars/MarkDuplicates.jar VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true INPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1097.dat OUTPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1098.dat METRICS_FILE=/udd/rerla/galaxy-central/database/job_working_directory/1032/dataset_1099_files/MarkDuplicates.metrics.txt REMOVE_DUPLICATES=true READ_NAME_REGEX="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*" OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 returned status 0 and stderr: 
139[Thu May 12 14:34:28 EDT 2011] net.sf.picard.sam.MarkDuplicates INPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1097.dat OUTPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1098.dat METRICS_FILE=/udd/rerla/galaxy-central/database/job_working_directory/1032/dataset_1099_files/MarkDuplicates.metrics.txt REMOVE_DUPLICATES=true ASSUME_SORTED=true READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VALIDATION_STRINGENCY=LENIENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 TMP_DIR=/tmp/rerla VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
140INFO	2011-05-12 14:34:28	MarkDuplicates	Start of doWork freeMemory: 8644632; totalMemory: 9109504; maxMemory: 1908932608
141INFO	2011-05-12 14:34:28	MarkDuplicates	Reading input file and constructing read end information.
142INFO	2011-05-12 14:34:28	MarkDuplicates	Will retain up to 7575129 data points before spilling to disk.
143INFO	2011-05-12 14:34:28	MarkDuplicates	Read 7 records. 0 pairs never matched.
144INFO	2011-05-12 14:34:29	MarkDuplicates	After buildSortedReadEndLists freeMemory: 8316168; totalMemory: 130351104; maxMemory: 1908932608
145INFO	2011-05-12 14:34:29	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
146INFO	2011-05-12 14:34:29	MarkDuplicates	Traversing read pair information and detecting duplicates.
147INFO	2011-05-12 14:34:29	MarkDuplicates	Traversing fragment information and detecting duplicates.
148INFO	2011-05-12 14:34:29	MarkDuplicates	Sorting list of duplicate records.
149INFO	2011-05-12 14:34:29	MarkDuplicates	After generateDuplicateIndexes freeMemory: 129615120; totalMemory: 607649792; maxMemory: 1908932608
150INFO	2011-05-12 14:34:29	MarkDuplicates	Marking 3 records as duplicates.
151INFO	2011-05-12 14:34:29	MarkDuplicates	Found 0 optical duplicate clusters.
152INFO	2011-05-12 14:34:29	MarkDuplicates	Before output close freeMemory: 128997520; totalMemory: 607649792; maxMemory: 1908932608
153INFO	2011-05-12 14:34:29	MarkDuplicates	After output close freeMemory: 128997280; totalMemory: 607649792; maxMemory: 1908932608
154[Thu May 12 14:34:29 EDT 2011] net.sf.picard.sam.MarkDuplicates done.
155Runtime.totalMemory()=607649792
156
157
158</pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> 
159generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html>
160