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-narrow--q_0.1 --extsize 300 -q 0.1 -c B7_input_d_s.bam --fix-bimodal -g 2380435629 # ARGUMENTS LIST: # name = B7_H3K4me1_vs_B7_input-macs-narrow--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 = 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 off # 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 16:56:06: 1000000 INFO @ Thu, 04 Oct 2018 16:56:12: 2000000 INFO @ Thu, 04 Oct 2018 16:56:18: 3000000 INFO @ Thu, 04 Oct 2018 16:56:25: 4000000 INFO @ Thu, 04 Oct 2018 16:56:31: 5000000 INFO @ Thu, 04 Oct 2018 16:56:37: 6000000 INFO @ Thu, 04 Oct 2018 16:56:43: 7000000 INFO @ Thu, 04 Oct 2018 16:56:49: 8000000 INFO @ Thu, 04 Oct 2018 16:56:56: 9000000 INFO @ Thu, 04 Oct 2018 16:57:02: 10000000 INFO @ Thu, 04 Oct 2018 16:57:08: 11000000 INFO @ Thu, 04 Oct 2018 16:57:14: 12000000 INFO @ Thu, 04 Oct 2018 16:57:20: 13000000 INFO @ Thu, 04 Oct 2018 16:57:27: 14000000 INFO @ Thu, 04 Oct 2018 16:57:33: 15000000 INFO @ Thu, 04 Oct 2018 16:57:39: 16000000 INFO @ Thu, 04 Oct 2018 16:57:45: 17000000 INFO @ Thu, 04 Oct 2018 16:57:51: 18000000 INFO @ Thu, 04 Oct 2018 16:57:57: 19000000 INFO @ Thu, 04 Oct 2018 16:58:04: 20000000 INFO @ Thu, 04 Oct 2018 16:58:10: 21000000 INFO @ Thu, 04 Oct 2018 16:58:16: 22000000 INFO @ Thu, 04 Oct 2018 16:58:22: 23000000 INFO @ Thu, 04 Oct 2018 16:58:28: 24000000 INFO @ Thu, 04 Oct 2018 16:58:34: 25000000 INFO @ Thu, 04 Oct 2018 16:58:41: 26000000 INFO @ Thu, 04 Oct 2018 16:58:47: 27000000 INFO @ Thu, 04 Oct 2018 16:58:53: 28000000 INFO @ Thu, 04 Oct 2018 16:58:59: 29000000 INFO @ Thu, 04 Oct 2018 16:59:05: 30000000 INFO @ Thu, 04 Oct 2018 16:59:11: 31000000 INFO @ Thu, 04 Oct 2018 16:59:18: 32000000 INFO @ Thu, 04 Oct 2018 16:59:24: 33000000 INFO @ Thu, 04 Oct 2018 16:59:30: 34000000 INFO @ Thu, 04 Oct 2018 16:59:37: 35000000 INFO @ Thu, 04 Oct 2018 16:59:42: 36000000 INFO @ Thu, 04 Oct 2018 16:59:45: #1.2 read input tags... INFO @ Thu, 04 Oct 2018 16:59:51: 1000000 INFO @ Thu, 04 Oct 2018 16:59:57: 2000000 INFO @ Thu, 04 Oct 2018 17:00:03: 3000000 INFO @ Thu, 04 Oct 2018 17:00:09: 4000000 INFO @ Thu, 04 Oct 2018 17:00:16: 5000000 INFO @ Thu, 04 Oct 2018 17:00:22: 6000000 INFO @ Thu, 04 Oct 2018 17:00:28: 7000000 INFO @ Thu, 04 Oct 2018 17:00:34: 8000000 INFO @ Thu, 04 Oct 2018 17:00:41: 9000000 INFO @ Thu, 04 Oct 2018 17:00:47: 10000000 INFO @ Thu, 04 Oct 2018 17:00:53: 11000000 INFO @ Thu, 04 Oct 2018 17:00:59: 12000000 INFO @ Thu, 04 Oct 2018 17:01:06: 13000000 INFO @ Thu, 04 Oct 2018 17:01:12: 14000000 INFO @ Thu, 04 Oct 2018 17:01:18: 15000000 INFO @ Thu, 04 Oct 2018 17:01:24: 16000000 INFO @ Thu, 04 Oct 2018 17:01:31: 17000000 INFO @ Thu, 04 Oct 2018 17:01:37: 18000000 INFO @ Thu, 04 Oct 2018 17:01:43: 19000000 INFO @ Thu, 04 Oct 2018 17:01:49: 20000000 INFO @ Thu, 04 Oct 2018 17:01:56: 21000000 INFO @ Thu, 04 Oct 2018 17:02:02: 22000000 INFO @ Thu, 04 Oct 2018 17:02:08: 23000000 INFO @ Thu, 04 Oct 2018 17:02:14: 24000000 INFO @ Thu, 04 Oct 2018 17:02:21: 25000000 INFO @ Thu, 04 Oct 2018 17:02:27: 26000000 INFO @ Thu, 04 Oct 2018 17:02:33: 27000000 INFO @ Thu, 04 Oct 2018 17:02:40: 28000000 INFO @ Thu, 04 Oct 2018 17:02:46: 29000000 INFO @ Thu, 04 Oct 2018 17:02:52: 30000000 INFO @ Thu, 04 Oct 2018 17:02:58: 31000000 INFO @ Thu, 04 Oct 2018 17:03:04: 32000000 INFO @ Thu, 04 Oct 2018 17:03:11: 33000000 INFO @ Thu, 04 Oct 2018 17:03:17: 34000000 INFO @ Thu, 04 Oct 2018 17:03:23: 35000000 INFO @ Thu, 04 Oct 2018 17:03:30: 36000000 INFO @ Thu, 04 Oct 2018 17:03:34: 37000000 INFO @ Thu, 04 Oct 2018 17:03:36: #1 tag size is determined as 75 bps INFO @ Thu, 04 Oct 2018 17:03:36: #1 tag size = 75 INFO @ Thu, 04 Oct 2018 17:03:36: #1 total tags in treatment: 35572353 INFO @ Thu, 04 Oct 2018 17:03:36: #1 user defined the maximum tags... INFO @ Thu, 04 Oct 2018 17:03:36: #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 17:03:37: #1 tags after filtering in treatment: 35572353 INFO @ Thu, 04 Oct 2018 17:03:37: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 04 Oct 2018 17:03:37: #1 total tags in control: 36326214 INFO @ Thu, 04 Oct 2018 17:03:37: #1 user defined the maximum tags... INFO @ Thu, 04 Oct 2018 17:03:37: #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 17:03:37: #1 tags after filtering in control: 36326214 INFO @ Thu, 04 Oct 2018 17:03:37: #1 Redundant rate of control: 0.00 INFO @ Thu, 04 Oct 2018 17:03:37: #1 finished! INFO @ Thu, 04 Oct 2018 17:03:37: #2 Build Peak Model... INFO @ Thu, 04 Oct 2018 17:03:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 04 Oct 2018 17:03:43: #2 number of paired peaks: 72281 INFO @ Thu, 04 Oct 2018 17:03:43: start model_add_line... INFO @ Thu, 04 Oct 2018 17:03:44: start X-correlation... INFO @ Thu, 04 Oct 2018 17:03:44: end of X-cor INFO @ Thu, 04 Oct 2018 17:03:44: #2 finished! INFO @ Thu, 04 Oct 2018 17:03:44: #2 predicted fragment length is 300 bps INFO @ Thu, 04 Oct 2018 17:03:44: #2 alternative fragment length(s) may be 1,300 bps INFO @ Thu, 04 Oct 2018 17:03:44: #2.2 Generate R script for model : B7_H3K4me1_vs_B7_input-macs-narrow--q_0.1_model.r INFO @ Thu, 04 Oct 2018 17:03:44: #3 Call peaks... INFO @ Thu, 04 Oct 2018 17:03:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 04 Oct 2018 17:06:13: #3 Call peaks for each chromosome... INFO @ Thu, 04 Oct 2018 17:07:50: #4 Write output xls file... B7_H3K4me1_vs_B7_input-macs-narrow--q_0.1_peaks.xls INFO @ Thu, 04 Oct 2018 17:07:52: #4 Write peak in narrowPeak format file... B7_H3K4me1_vs_B7_input-macs-narrow--q_0.1_peaks.narrowPeak INFO @ Thu, 04 Oct 2018 17:07:53: #4 Write summits bed file... B7_H3K4me1_vs_B7_input-macs-narrow--q_0.1_summits.bed INFO @ Thu, 04 Oct 2018 17:07:54: Done!