INFO @ Thu, 04 Oct 2018 16:56:00: # Command line: callpeak -t B7_H3K4me1_d_s.bam -f BAM -n B7_H3K4me1_vs_B7_input-macs-broad--q_0.1 --extsize 300 -q 0.1 --broad -c B7_input_d_s.bam --fix-bimodal -g 2380435629 # ARGUMENTS LIST: # name = B7_H3K4me1_vs_B7_input-macs-broad--q_0.1 # format = BAM # ChIP-seq file = ['B7_H3K4me1_d_s.bam'] # control file = ['B7_input_d_s.bam'] # effective genome size = 2.38e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff for narrow/strong regions = 1.00e-01 # qvalue cutoff for broad/weak regions = 1.00e-01 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 1000 bps and 10000 bps # Broad region calling is on # Paired-End mode is off INFO @ Thu, 04 Oct 2018 16:56:00: #1 read tag files... INFO @ Thu, 04 Oct 2018 16:56:00: #1 read treatment tags... INFO @ Thu, 04 Oct 2018 16:56:05: 1000000 INFO @ Thu, 04 Oct 2018 16:56:10: 2000000 INFO @ Thu, 04 Oct 2018 16:56:15: 3000000 INFO @ Thu, 04 Oct 2018 16:56:20: 4000000 INFO @ Thu, 04 Oct 2018 16:56:25: 5000000 INFO @ Thu, 04 Oct 2018 16:56:30: 6000000 INFO @ Thu, 04 Oct 2018 16:56:35: 7000000 INFO @ Thu, 04 Oct 2018 16:56:40: 8000000 INFO @ Thu, 04 Oct 2018 16:56:45: 9000000 INFO @ Thu, 04 Oct 2018 16:56:50: 10000000 INFO @ Thu, 04 Oct 2018 16:56:55: 11000000 INFO @ Thu, 04 Oct 2018 16:57:00: 12000000 INFO @ Thu, 04 Oct 2018 16:57:05: 13000000 INFO @ Thu, 04 Oct 2018 16:57:10: 14000000 INFO @ Thu, 04 Oct 2018 16:57:15: 15000000 INFO @ Thu, 04 Oct 2018 16:57:20: 16000000 INFO @ Thu, 04 Oct 2018 16:57:25: 17000000 INFO @ Thu, 04 Oct 2018 16:57:30: 18000000 INFO @ Thu, 04 Oct 2018 16:57:35: 19000000 INFO @ Thu, 04 Oct 2018 16:57:40: 20000000 INFO @ Thu, 04 Oct 2018 16:57:45: 21000000 INFO @ Thu, 04 Oct 2018 16:57:50: 22000000 INFO @ Thu, 04 Oct 2018 16:57:55: 23000000 INFO @ Thu, 04 Oct 2018 16:58:00: 24000000 INFO @ Thu, 04 Oct 2018 16:58:05: 25000000 INFO @ Thu, 04 Oct 2018 16:58:11: 26000000 INFO @ Thu, 04 Oct 2018 16:58:16: 27000000 INFO @ Thu, 04 Oct 2018 16:58:21: 28000000 INFO @ Thu, 04 Oct 2018 16:58:26: 29000000 INFO @ Thu, 04 Oct 2018 16:58:30: 30000000 INFO @ Thu, 04 Oct 2018 16:58:36: 31000000 INFO @ Thu, 04 Oct 2018 16:58:41: 32000000 INFO @ Thu, 04 Oct 2018 16:58:46: 33000000 INFO @ Thu, 04 Oct 2018 16:58:51: 34000000 INFO @ Thu, 04 Oct 2018 16:58:56: 35000000 INFO @ Thu, 04 Oct 2018 16:59:00: 36000000 INFO @ Thu, 04 Oct 2018 16:59:02: #1.2 read input tags... INFO @ Thu, 04 Oct 2018 16:59:07: 1000000 INFO @ Thu, 04 Oct 2018 16:59:12: 2000000 INFO @ Thu, 04 Oct 2018 16:59:17: 3000000 INFO @ Thu, 04 Oct 2018 16:59:22: 4000000 INFO @ Thu, 04 Oct 2018 16:59:27: 5000000 INFO @ Thu, 04 Oct 2018 16:59:32: 6000000 INFO @ Thu, 04 Oct 2018 16:59:38: 7000000 INFO @ Thu, 04 Oct 2018 16:59:43: 8000000 INFO @ Thu, 04 Oct 2018 16:59:48: 9000000 INFO @ Thu, 04 Oct 2018 16:59:53: 10000000 INFO @ Thu, 04 Oct 2018 16:59:58: 11000000 INFO @ Thu, 04 Oct 2018 17:00:03: 12000000 INFO @ Thu, 04 Oct 2018 17:00:08: 13000000 INFO @ Thu, 04 Oct 2018 17:00:13: 14000000 INFO @ Thu, 04 Oct 2018 17:00:18: 15000000 INFO @ Thu, 04 Oct 2018 17:00:23: 16000000 INFO @ Thu, 04 Oct 2018 17:00:28: 17000000 INFO @ Thu, 04 Oct 2018 17:00:33: 18000000 INFO @ Thu, 04 Oct 2018 17:00:38: 19000000 INFO @ Thu, 04 Oct 2018 17:00:43: 20000000 INFO @ Thu, 04 Oct 2018 17:00:48: 21000000 INFO @ Thu, 04 Oct 2018 17:00:53: 22000000 INFO @ Thu, 04 Oct 2018 17:00:58: 23000000 INFO @ Thu, 04 Oct 2018 17:01:03: 24000000 INFO @ Thu, 04 Oct 2018 17:01:08: 25000000 INFO @ Thu, 04 Oct 2018 17:01:13: 26000000 INFO @ Thu, 04 Oct 2018 17:01:18: 27000000 INFO @ Thu, 04 Oct 2018 17:01:23: 28000000 INFO @ Thu, 04 Oct 2018 17:01:28: 29000000 INFO @ Thu, 04 Oct 2018 17:01:33: 30000000 INFO @ Thu, 04 Oct 2018 17:01:38: 31000000 INFO @ Thu, 04 Oct 2018 17:01:43: 32000000 INFO @ Thu, 04 Oct 2018 17:01:48: 33000000 INFO @ Thu, 04 Oct 2018 17:01:53: 34000000 INFO @ Thu, 04 Oct 2018 17:01:58: 35000000 INFO @ Thu, 04 Oct 2018 17:02:03: 36000000 INFO @ Thu, 04 Oct 2018 17:02:07: 37000000 INFO @ Thu, 04 Oct 2018 17:02:09: #1 tag size is determined as 75 bps INFO @ Thu, 04 Oct 2018 17:02:09: #1 tag size = 75 INFO @ Thu, 04 Oct 2018 17:02:09: #1 total tags in treatment: 35572353 INFO @ Thu, 04 Oct 2018 17:02:09: #1 user defined the maximum tags... INFO @ Thu, 04 Oct 2018 17:02:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 04 Oct 2018 17:02:09: #1 tags after filtering in treatment: 35572353 INFO @ Thu, 04 Oct 2018 17:02:09: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 04 Oct 2018 17:02:09: #1 total tags in control: 36326214 INFO @ Thu, 04 Oct 2018 17:02:09: #1 user defined the maximum tags... INFO @ Thu, 04 Oct 2018 17:02:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 04 Oct 2018 17:02:10: #1 tags after filtering in control: 36326214 INFO @ Thu, 04 Oct 2018 17:02:10: #1 Redundant rate of control: 0.00 INFO @ Thu, 04 Oct 2018 17:02:10: #1 finished! INFO @ Thu, 04 Oct 2018 17:02:10: #2 Build Peak Model... INFO @ Thu, 04 Oct 2018 17:02:10: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 04 Oct 2018 17:02:15: #2 number of paired peaks: 72281 INFO @ Thu, 04 Oct 2018 17:02:15: start model_add_line... INFO @ Thu, 04 Oct 2018 17:02:16: start X-correlation... INFO @ Thu, 04 Oct 2018 17:02:16: end of X-cor INFO @ Thu, 04 Oct 2018 17:02:16: #2 finished! INFO @ Thu, 04 Oct 2018 17:02:16: #2 predicted fragment length is 300 bps INFO @ Thu, 04 Oct 2018 17:02:16: #2 alternative fragment length(s) may be 1,300 bps INFO @ Thu, 04 Oct 2018 17:02:16: #2.2 Generate R script for model : B7_H3K4me1_vs_B7_input-macs-broad--q_0.1_model.r INFO @ Thu, 04 Oct 2018 17:02:16: #3 Call peaks... INFO @ Thu, 04 Oct 2018 17:02:16: #3 Call broad peaks with given level1 -log10qvalue cutoff and level2: 1.000000, 1.000000... INFO @ Thu, 04 Oct 2018 17:02:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 04 Oct 2018 17:04:49: #3 Call peaks for each chromosome... INFO @ Thu, 04 Oct 2018 17:07:42: #4 Write output xls file... B7_H3K4me1_vs_B7_input-macs-broad--q_0.1_peaks.xls INFO @ Thu, 04 Oct 2018 17:07:43: #4 Write broad peak in broadPeak format file... B7_H3K4me1_vs_B7_input-macs-broad--q_0.1_peaks.broadPeak INFO @ Thu, 04 Oct 2018 17:07:44: #4 Write broad peak in bed12/gappedPeak format file... B7_H3K4me1_vs_B7_input-macs-broad--q_0.1_peaks.gappedPeak INFO @ Thu, 04 Oct 2018 17:07:45: Done!