Additional Files:
Messages from MACS2:
INFO @ Tue, 24 Jan 2017 12:19:10:
# 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
# ARGUMENTS LIST:
# name = MACS2
# format = BED
# ChIP-seq file = ['/tmp/tmp1QIUtc/files/000/dataset_1.dat']
# control file = ['/tmp/tmp1QIUtc/files/000/dataset_2.dat']
# effective genome size = 3.30e+09
# 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
INFO @ Tue, 24 Jan 2017 12:19:10: #1 read tag files...
INFO @ Tue, 24 Jan 2017 12:19:10: #1 read treatment tags...
INFO @ Tue, 24 Jan 2017 12:19:10: #1.2 read input tags...
INFO @ Tue, 24 Jan 2017 12:19:10: #1 tag size is determined as 100 bps
INFO @ Tue, 24 Jan 2017 12:19:10: #1 tag size = 100
INFO @ Tue, 24 Jan 2017 12:19:10: #1 total tags in treatment: 199977
INFO @ Tue, 24 Jan 2017 12:19:10: #1 user defined the maximum tags...
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)
INFO @ Tue, 24 Jan 2017 12:19:10: #1 tags after filtering in treatment: 199583
INFO @ Tue, 24 Jan 2017 12:19:10: #1 Redundant rate of treatment: 0.00
INFO @ Tue, 24 Jan 2017 12:19:10: #1 total tags in control: 199978
INFO @ Tue, 24 Jan 2017 12:19:10: #1 user defined the maximum tags...
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)
INFO @ Tue, 24 Jan 2017 12:19:10: #1 tags after filtering in control: 199867
INFO @ Tue, 24 Jan 2017 12:19:10: #1 Redundant rate of control: 0.00
INFO @ Tue, 24 Jan 2017 12:19:10: #1 finished!
INFO @ Tue, 24 Jan 2017 12:19:10: #2 Build Peak Model...
INFO @ Tue, 24 Jan 2017 12:19:10: #2 looking for paired plus/minus strand peaks...
INFO @ Tue, 24 Jan 2017 12:19:11: #2 number of paired peaks: 4488
INFO @ Tue, 24 Jan 2017 12:19:11: start model_add_line...
INFO @ Tue, 24 Jan 2017 12:19:11: start X-correlation...
INFO @ Tue, 24 Jan 2017 12:19:11: end of X-cor
INFO @ Tue, 24 Jan 2017 12:19:11: #2 finished!
INFO @ Tue, 24 Jan 2017 12:19:11: #2 predicted fragment length is 254 bps
INFO @ Tue, 24 Jan 2017 12:19:11: #2 alternative fragment length(s) may be 254 bps
INFO @ Tue, 24 Jan 2017 12:19:11: #2.2 Generate R script for model : MACS2_model.r
INFO @ Tue, 24 Jan 2017 12:19:11: #3 Call peaks...
INFO @ Tue, 24 Jan 2017 12:19:11: #3 Pre-compute pvalue-qvalue table...
INFO @ Tue, 24 Jan 2017 12:19:12: #3 Call peaks for each chromosome...
INFO @ Tue, 24 Jan 2017 12:19:13: #4 Write output xls file... MACS2_peaks.xls
INFO @ Tue, 24 Jan 2017 12:19:13: #4 Write peak in narrowPeak format file... MACS2_peaks.narrowPeak
INFO @ Tue, 24 Jan 2017 12:19:13: #4 Write summits bed file... MACS2_summits.bed
INFO @ Tue, 24 Jan 2017 12:19:13: Done!