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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e
author iuc
date Mon, 06 Feb 2017 02:30:37 -0500
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   <title>Additional output created by MACS2</title>
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<h1>Additional Files:</h1>
<table class="fileList">
<tr><td class="file"><a href="MACS2_model.pdf">model.pdf</a></td></tr>
<tr><td class="file"><a href="MACS2_summits.bed">summits.bed</a></td></tr>
<tr><td class="file"><a href="MACS2_model.r">model.r</a></td></tr>
<tr><td class="file"><a href="MACS2_peaks.narrowPeak">peaks.narrowPeak</a></td></tr>
<tr><td class="file"><a href="MACS2_model.r.log">model.r.log</a></td></tr>
<tr><td class="file"><a href="MACS2_peaks.xls">peaks.xls</a></td></tr>
</table>
<h3>Messages from MACS2:</h3>
INFO  @ Tue, 24 Jan 2017 12:19:10: <br># Command line: callpeak --name MACS2 -t /tmp/tmp1QIUtc/files/000/dataset_1.dat -c /tmp/tmp1QIUtc/files/000/dataset_2.dat --format=BED --gsize 3300000000 --bw=300 --qvalue 0.05<br># ARGUMENTS LIST:<br># name = MACS2<br># format = BED<br># ChIP-seq file = ['/tmp/tmp1QIUtc/files/000/dataset_1.dat']<br># control file = ['/tmp/tmp1QIUtc/files/000/dataset_2.dat']<br># effective genome size = 3.30e+09<br># band width = 300<br># model fold = [5, 50]<br># qvalue cutoff = 5.00e-02<br># Larger dataset will be scaled towards smaller dataset.<br># Range for calculating regional lambda is: 1000 bps and 10000 bps<br># Broad region calling is off<br># Paired-End mode is off<br> <br>INFO  @ Tue, 24 Jan 2017 12:19:10: #1 read tag files... <br>INFO  @ Tue, 24 Jan 2017 12:19:10: #1 read treatment tags... <br>INFO  @ Tue, 24 Jan 2017 12:19:10: #1.2 read input tags... <br>INFO  @ Tue, 24 Jan 2017 12:19:10: #1 tag size is determined as 100 bps <br>INFO  @ Tue, 24 Jan 2017 12:19:10: #1 tag size = 100 <br>INFO  @ Tue, 24 Jan 2017 12:19:10: #1  total tags in treatment: 199977 <br>INFO  @ Tue, 24 Jan 2017 12:19:10: #1 user defined the maximum tags... <br>INFO  @ Tue, 24 Jan 2017 12:19:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) <br>INFO  @ Tue, 24 Jan 2017 12:19:10: #1  tags after filtering in treatment: 199583 <br>INFO  @ Tue, 24 Jan 2017 12:19:10: #1  Redundant rate of treatment: 0.00 <br>INFO  @ Tue, 24 Jan 2017 12:19:10: #1  total tags in control: 199978 <br>INFO  @ Tue, 24 Jan 2017 12:19:10: #1 user defined the maximum tags... <br>INFO  @ Tue, 24 Jan 2017 12:19:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) <br>INFO  @ Tue, 24 Jan 2017 12:19:10: #1  tags after filtering in control: 199867 <br>INFO  @ Tue, 24 Jan 2017 12:19:10: #1  Redundant rate of control: 0.00 <br>INFO  @ Tue, 24 Jan 2017 12:19:10: #1 finished! <br>INFO  @ Tue, 24 Jan 2017 12:19:10: #2 Build Peak Model... <br>INFO  @ Tue, 24 Jan 2017 12:19:10: #2 looking for paired plus/minus strand peaks... <br>INFO  @ Tue, 24 Jan 2017 12:19:11: #2 number of paired peaks: 4488 <br>INFO  @ Tue, 24 Jan 2017 12:19:11: start model_add_line... <br>INFO  @ Tue, 24 Jan 2017 12:19:11: start X-correlation... <br>INFO  @ Tue, 24 Jan 2017 12:19:11: end of X-cor <br>INFO  @ Tue, 24 Jan 2017 12:19:11: #2 finished! <br>INFO  @ Tue, 24 Jan 2017 12:19:11: #2 predicted fragment length is 254 bps <br>INFO  @ Tue, 24 Jan 2017 12:19:11: #2 alternative fragment length(s) may be 254 bps <br>INFO  @ Tue, 24 Jan 2017 12:19:11: #2.2 Generate R script for model : MACS2_model.r <br>INFO  @ Tue, 24 Jan 2017 12:19:11: #3 Call peaks... <br>INFO  @ Tue, 24 Jan 2017 12:19:11: #3 Pre-compute pvalue-qvalue table... <br>INFO  @ Tue, 24 Jan 2017 12:19:12: #3 Call peaks for each chromosome... <br>INFO  @ Tue, 24 Jan 2017 12:19:13: #4 Write output xls file... MACS2_peaks.xls <br>INFO  @ Tue, 24 Jan 2017 12:19:13: #4 Write peak in narrowPeak format file... MACS2_peaks.narrowPeak <br>INFO  @ Tue, 24 Jan 2017 12:19:13: #4 Write summits bed file... MACS2_summits.bed <br>INFO  @ Tue, 24 Jan 2017 12:19:13: Done! <br>
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