INFO  @ Tue, 05 Sep 2017 14:15:05: 
# Command line: callpeak -t /scratch/AG_Ohler/rebecca/poznan_ChIPseq_analysis/chipseq_ctcf_chr21/starchr21rep1/Aligned.out.coordSrt.rmdup.uniq.chrfilt.bed /scratch/AG_Ohler/rebecca/poznan_ChIPseq_analysis/chipseq_ctcf_chr21/starchr21rep2/Aligned.out.coordSrt.rmdup.uniq.chrfilt.bed -c /scratch/AG_Ohler/rebecca/poznan_ChIPseq_analysis/chipseq_ctcf_chr21/starchr21control1/Aligned.out.coordSrt.rmdup.uniq.chrfilt.bed /scratch/AG_Ohler/rebecca/poznan_ChIPseq_analysis/chipseq_ctcf_chr21/starchr21control2/Aligned.out.coordSrt.rmdup.uniq.chrfilt.bed -f BED -g hs -n /scratch/AG_Ohler/rebecca/poznan_ChIPseq_analysis/chipseq_ctcf_chr21/testmacs2/macs2_chip -B -q 0.01
# ARGUMENTS LIST:
# name = /scratch/AG_Ohler/rebecca/poznan_ChIPseq_analysis/chipseq_ctcf_chr21/testmacs2/macs2_chip
# format = BED
# ChIP-seq file = ['/scratch/AG_Ohler/rebecca/poznan_ChIPseq_analysis/chipseq_ctcf_chr21/starchr21rep1/Aligned.out.coordSrt.rmdup.uniq.chrfilt.bed', '/scratch/AG_Ohler/rebecca/poznan_ChIPseq_analysis/chipseq_ctcf_chr21/starchr21rep2/Aligned.out.coordSrt.rmdup.uniq.chrfilt.bed']
# control file = ['/scratch/AG_Ohler/rebecca/poznan_ChIPseq_analysis/chipseq_ctcf_chr21/starchr21control1/Aligned.out.coordSrt.rmdup.uniq.chrfilt.bed', '/scratch/AG_Ohler/rebecca/poznan_ChIPseq_analysis/chipseq_ctcf_chr21/starchr21control2/Aligned.out.coordSrt.rmdup.uniq.chrfilt.bed']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# qvalue cutoff = 1.00e-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
 
INFO  @ Tue, 05 Sep 2017 14:15:05: #1 read tag files... 
INFO  @ Tue, 05 Sep 2017 14:15:05: #1 read treatment tags... 
INFO  @ Tue, 05 Sep 2017 14:15:10: #1.2 read input tags... 
INFO  @ Tue, 05 Sep 2017 14:15:13: #1 tag size is determined as 36 bps 
INFO  @ Tue, 05 Sep 2017 14:15:13: #1 tag size = 36 
INFO  @ Tue, 05 Sep 2017 14:15:13: #1  total tags in treatment: 258211 
INFO  @ Tue, 05 Sep 2017 14:15:13: #1 user defined the maximum tags... 
INFO  @ Tue, 05 Sep 2017 14:15:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 
INFO  @ Tue, 05 Sep 2017 14:15:13: #1  tags after filtering in treatment: 255516 
INFO  @ Tue, 05 Sep 2017 14:15:13: #1  Redundant rate of treatment: 0.01 
INFO  @ Tue, 05 Sep 2017 14:15:13: #1  total tags in control: 140881 
INFO  @ Tue, 05 Sep 2017 14:15:13: #1 user defined the maximum tags... 
INFO  @ Tue, 05 Sep 2017 14:15:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 
INFO  @ Tue, 05 Sep 2017 14:15:13: #1  tags after filtering in control: 140703 
INFO  @ Tue, 05 Sep 2017 14:15:13: #1  Redundant rate of control: 0.00 
INFO  @ Tue, 05 Sep 2017 14:15:13: #1 finished! 
INFO  @ Tue, 05 Sep 2017 14:15:13: #2 Build Peak Model... 
INFO  @ Tue, 05 Sep 2017 14:15:13: #2 looking for paired plus/minus strand peaks... 
INFO  @ Tue, 05 Sep 2017 14:15:13: #2 number of paired peaks: 801 
WARNING @ Tue, 05 Sep 2017 14:15:13: Fewer paired peaks (801) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 801 pairs to build model! 
INFO  @ Tue, 05 Sep 2017 14:15:13: start model_add_line... 
INFO  @ Tue, 05 Sep 2017 14:15:13: start X-correlation... 
INFO  @ Tue, 05 Sep 2017 14:15:13: end of X-cor 
INFO  @ Tue, 05 Sep 2017 14:15:13: #2 finished! 
INFO  @ Tue, 05 Sep 2017 14:15:13: #2 predicted fragment length is 295 bps 
INFO  @ Tue, 05 Sep 2017 14:15:13: #2 alternative fragment length(s) may be 295,534 bps 
INFO  @ Tue, 05 Sep 2017 14:15:13: #2.2 Generate R script for model : /scratch/AG_Ohler/rebecca/poznan_ChIPseq_analysis/chipseq_ctcf_chr21/testmacs2/macs2_chip_model.r 
INFO  @ Tue, 05 Sep 2017 14:15:13: #3 Call peaks... 
INFO  @ Tue, 05 Sep 2017 14:15:13: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 05 Sep 2017 14:15:14: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 05 Sep 2017 14:15:14: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /scratch/AG_Ohler/rebecca/poznan_ChIPseq_analysis/chipseq_ctcf_chr21/testmacs2/macs2_chip_treat_pileup.bdg 
INFO  @ Tue, 05 Sep 2017 14:15:14: #3   Write bedGraph files for control lambda (after scaling if necessary)... /scratch/AG_Ohler/rebecca/poznan_ChIPseq_analysis/chipseq_ctcf_chr21/testmacs2/macs2_chip_control_lambda.bdg 
INFO  @ Tue, 05 Sep 2017 14:15:14: #3   Pileup will be based on sequencing depth in control. 
INFO  @ Tue, 05 Sep 2017 14:15:14: #3 Call peaks for each chromosome... 
INFO  @ Tue, 05 Sep 2017 14:15:18: #4 Write output xls file... /scratch/AG_Ohler/rebecca/poznan_ChIPseq_analysis/chipseq_ctcf_chr21/testmacs2/macs2_chip_peaks.xls 
INFO  @ Tue, 05 Sep 2017 14:15:18: #4 Write peak in narrowPeak format file... /scratch/AG_Ohler/rebecca/poznan_ChIPseq_analysis/chipseq_ctcf_chr21/testmacs2/macs2_chip_peaks.narrowPeak 
INFO  @ Tue, 05 Sep 2017 14:15:18: #4 Write summits bed file... /scratch/AG_Ohler/rebecca/poznan_ChIPseq_analysis/chipseq_ctcf_chr21/testmacs2/macs2_chip_summits.bed 
INFO  @ Tue, 05 Sep 2017 14:15:18: Done! 
