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MACS.out
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56 lines (55 loc) · 3.43 KB
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INFO @ Mon, 26 Jul 2021 15:35:18:
# Command line: callpeak -t SRR576933.sam -c SRR576938.sam --format SAM --gsize 4641652 --name macs2 --bw 400 --keep-dup 2 --bdg --nomodel --extsize 200
# ARGUMENTS LIST:
# name = macs2
# format = SAM
# ChIP-seq file = ['SRR576933.sam']
# control file = ['SRR576938.sam']
# effective genome size = 4.64e+06
# band width = 400
# model fold = [5, 50]
# qvalue cutoff = 5.00e-02
# The maximum gap between significant sites is assigned as the read length/tag size.
# The minimum length of peaks is assigned as the predicted fragment length "d".
# 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
INFO @ Mon, 26 Jul 2021 15:35:18: #1 read tag files...
INFO @ Mon, 26 Jul 2021 15:35:18: #1 read treatment tags...
INFO @ Mon, 26 Jul 2021 15:35:20: 2000000
INFO @ Mon, 26 Jul 2021 15:35:24: 3000000
INFO @ Mon, 26 Jul 2021 15:35:26: #1.2 read input tags...
INFO @ Mon, 26 Jul 2021 15:35:32: 1000000
INFO @ Mon, 26 Jul 2021 15:35:40: 2000000
INFO @ Mon, 26 Jul 2021 15:35:48: 3000000
INFO @ Mon, 26 Jul 2021 15:35:56: 4000000
INFO @ Mon, 26 Jul 2021 15:36:03: 5000000
INFO @ Mon, 26 Jul 2021 15:36:05: 6000000
INFO @ Mon, 26 Jul 2021 15:36:07: #1 tag size is determined as 35 bps
INFO @ Mon, 26 Jul 2021 15:36:07: #1 tag size = 35.0
INFO @ Mon, 26 Jul 2021 15:36:07: #1 total tags in treatment: 2242359
INFO @ Mon, 26 Jul 2021 15:36:07: #1 user defined the maximum tags...
INFO @ Mon, 26 Jul 2021 15:36:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 2 tag(s)
INFO @ Mon, 26 Jul 2021 15:36:07: #1 tags after filtering in treatment: 1571169
INFO @ Mon, 26 Jul 2021 15:36:07: #1 Redundant rate of treatment: 0.30
INFO @ Mon, 26 Jul 2021 15:36:07: #1 total tags in control: 6392931
INFO @ Mon, 26 Jul 2021 15:36:07: #1 user defined the maximum tags...
INFO @ Mon, 26 Jul 2021 15:36:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 2 tag(s)
INFO @ Mon, 26 Jul 2021 15:36:07: #1 tags after filtering in control: 5751120
INFO @ Mon, 26 Jul 2021 15:36:07: #1 Redundant rate of control: 0.10
INFO @ Mon, 26 Jul 2021 15:36:07: #1 finished!
INFO @ Mon, 26 Jul 2021 15:36:07: #2 Build Peak Model...
INFO @ Mon, 26 Jul 2021 15:36:07: #2 Skipped...
INFO @ Mon, 26 Jul 2021 15:36:07: #2 Use 200 as fragment length
INFO @ Mon, 26 Jul 2021 15:36:07: #3 Call peaks...
INFO @ Mon, 26 Jul 2021 15:36:07: #3 Pre-compute pvalue-qvalue table...
INFO @ Mon, 26 Jul 2021 15:36:17: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Mon, 26 Jul 2021 15:36:17: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... macs2_treat_pileup.bdg
INFO @ Mon, 26 Jul 2021 15:36:17: #3 Write bedGraph files for control lambda (after scaling if necessary)... macs2_control_lambda.bdg
INFO @ Mon, 26 Jul 2021 15:36:17: #3 Pileup will be based on sequencing depth in treatment.
INFO @ Mon, 26 Jul 2021 15:36:17: #3 Call peaks for each chromosome...
INFO @ Mon, 26 Jul 2021 15:36:24: #4 Write output xls file... macs2_peaks.xls
INFO @ Mon, 26 Jul 2021 15:36:24: #4 Write peak in narrowPeak format file... macs2_peaks.narrowPeak
INFO @ Mon, 26 Jul 2021 15:36:24: #4 Write summits bed file... macs2_summits.bed
INFO @ Mon, 26 Jul 2021 15:36:24: Done!