Mercurial > repos > pjbriggs > macs21
view test-data/test_MACS2.1.1_bw_html_report.zip @ 3:4124781932db draft
Updated to MACS 2.1.1 and use conda for dependency resolution.
| author | pjbriggs |
|---|---|
| date | Tue, 20 Mar 2018 11:25:04 -0400 |
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<html><head><title>Additional output created by MACS (test_MACS2.1.1)</title></head><body><h3>Additional Files:</h3><p><ul> <li><a href="test_MACS2.1.1_peaks.xls">test_MACS2.1.1_peaks.xls</a></li> <li><a href="test_MACS2.1.1_treat_pileup.bdg.clipped">test_MACS2.1.1_treat_pileup.bdg.clipped</a></li> <li><a href="test_MACS2.1.1_treat_pileup.bdg.clipped.sorted">test_MACS2.1.1_treat_pileup.bdg.clipped.sorted</a></li> </ul></p> <h3>Messages from MACS:</h3> <p><pre>INFO @ Tue, 20 Mar 2018 14:21:47: # Command line: callpeak -t /tmp/tmpHxmla3/files/000/dataset_9.dat -c /tmp/tmpHxmla3/files/000/dataset_10.dat --format=BED --name=test_MACS2.1.1 --bw=300 --gsize=775000000.0 --nomodel --extsize=243 --qvalue=0.05 -B --SPMR --mfold 5 50 --keep-dup 1 # ARGUMENTS LIST: # name = test_MACS2.1.1 # format = BED # ChIP-seq file = ['/tmp/tmpHxmla3/files/000/dataset_9.dat'] # control file = ['/tmp/tmpHxmla3/files/000/dataset_10.dat'] # effective genome size = 7.75e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 5.00e-02 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 1000 bps and 10000 bps # Broad region calling is off # Paired-End mode is off # MACS will save fragment pileup signal per million reads INFO @ Tue, 20 Mar 2018 14:21:47: #1 read tag files... INFO @ Tue, 20 Mar 2018 14:21:47: #1 read treatment tags... INFO @ Tue, 20 Mar 2018 14:21:47: #1.2 read input tags... INFO @ Tue, 20 Mar 2018 14:21:47: #1 tag size is determined as 50 bps INFO @ Tue, 20 Mar 2018 14:21:47: #1 tag size = 50 INFO @ Tue, 20 Mar 2018 14:21:47: #1 total tags in treatment: 50 INFO @ Tue, 20 Mar 2018 14:21:47: #1 user defined the maximum tags... INFO @ Tue, 20 Mar 2018 14:21:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 20 Mar 2018 14:21:47: #1 tags after filtering in treatment: 50 INFO @ Tue, 20 Mar 2018 14:21:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 20 Mar 2018 14:21:47: #1 total tags in control: 50 INFO @ Tue, 20 Mar 2018 14:21:47: #1 user defined the maximum tags... INFO @ Tue, 20 Mar 2018 14:21:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 20 Mar 2018 14:21:47: #1 tags after filtering in control: 50 INFO @ Tue, 20 Mar 2018 14:21:47: #1 Redundant rate of control: 0.00 INFO @ Tue, 20 Mar 2018 14:21:47: #1 finished! INFO @ Tue, 20 Mar 2018 14:21:47: #2 Build Peak Model... INFO @ Tue, 20 Mar 2018 14:21:47: #2 Skipped... INFO @ Tue, 20 Mar 2018 14:21:47: #2 Use 243 as fragment length INFO @ Tue, 20 Mar 2018 14:21:47: #3 Call peaks... INFO @ Tue, 20 Mar 2018 14:21:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 20 Mar 2018 14:21:47: #3 In the peak calling step, the following will be performed simultaneously: INFO @ Tue, 20 Mar 2018 14:21:47: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... test_MACS2.1.1_treat_pileup.bdg INFO @ Tue, 20 Mar 2018 14:21:47: #3 Write bedGraph files for control lambda (after scaling if necessary)... test_MACS2.1.1_control_lambda.bdg INFO @ Tue, 20 Mar 2018 14:21:47: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. INFO @ Tue, 20 Mar 2018 14:21:47: #3 Call peaks for each chromosome... INFO @ Tue, 20 Mar 2018 14:21:47: #4 Write output xls file... test_MACS2.1.1_peaks.xls INFO @ Tue, 20 Mar 2018 14:21:47: #4 Write peak in narrowPeak format file... test_MACS2.1.1_peaks.narrowPeak INFO @ Tue, 20 Mar 2018 14:21:47: #4 Write summits bed file... test_MACS2.1.1_summits.bed INFO @ Tue, 20 Mar 2018 14:21:47: Done! </pre></p> </body></html>