Inactive Modules: 1) slurm INFO @ Mon, 24 Feb 2025 15:08:21: # Command line: callpeak -t T1P_HA_hg38_sorted.bam -c T1P_IgG_hg38_sorted.bam -f BAM -g hs -n T1P_HA_hg38_callpeaks1 --call-summits -q 0.05 --bdg # ARGUMENTS LIST: # name = T1P_HA_hg38_callpeaks1 # format = BAM # ChIP-seq file = ['T1P_HA_hg38_sorted.bam'] # control file = ['T1P_IgG_hg38_sorted.bam'] # effective genome size = 2.70e+09 # band width = 300 # 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 # Searching for subpeak summits is on INFO @ Mon, 24 Feb 2025 15:08:21: #1 read tag files... INFO @ Mon, 24 Feb 2025 15:08:21: #1 read treatment tags... INFO @ Mon, 24 Feb 2025 15:08:27: 1000000 INFO @ Mon, 24 Feb 2025 15:08:32: 2000000 INFO @ Mon, 24 Feb 2025 15:08:46: 2880259 reads have been read. INFO @ Mon, 24 Feb 2025 15:08:46: #1.2 read input tags... INFO @ Mon, 24 Feb 2025 15:08:52: 1000000 INFO @ Mon, 24 Feb 2025 15:08:57: 2000000 INFO @ Mon, 24 Feb 2025 15:09:03: 3000000 INFO @ Mon, 24 Feb 2025 15:09:09: 4000000 INFO @ Mon, 24 Feb 2025 15:09:14: 5000000 INFO @ Mon, 24 Feb 2025 15:09:20: 6000000 INFO @ Mon, 24 Feb 2025 15:09:40: 6890662 reads have been read. INFO @ Mon, 24 Feb 2025 15:09:40: #1 tag size is determined as 101 bps INFO @ Mon, 24 Feb 2025 15:09:40: #1 tag size = 101.0 INFO @ Mon, 24 Feb 2025 15:09:40: #1 total tags in treatment: 2880259 INFO @ Mon, 24 Feb 2025 15:09:40: #1 user defined the maximum tags... INFO @ Mon, 24 Feb 2025 15:09:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 24 Feb 2025 15:09:40: #1 tags after filtering in treatment: 2807962 INFO @ Mon, 24 Feb 2025 15:09:40: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 24 Feb 2025 15:09:40: #1 total tags in control: 6890662 INFO @ Mon, 24 Feb 2025 15:09:40: #1 user defined the maximum tags... INFO @ Mon, 24 Feb 2025 15:09:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 24 Feb 2025 15:09:40: #1 tags after filtering in control: 6700819 INFO @ Mon, 24 Feb 2025 15:09:40: #1 Redundant rate of control: 0.03 INFO @ Mon, 24 Feb 2025 15:09:40: #1 finished! INFO @ Mon, 24 Feb 2025 15:09:40: #2 Build Peak Model... INFO @ Mon, 24 Feb 2025 15:09:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 24 Feb 2025 15:09:43: #2 number of paired peaks: 19958 INFO @ Mon, 24 Feb 2025 15:09:43: start model_add_line... INFO @ Mon, 24 Feb 2025 15:09:43: start X-correlation... INFO @ Mon, 24 Feb 2025 15:09:43: end of X-cor INFO @ Mon, 24 Feb 2025 15:09:43: #2 finished! INFO @ Mon, 24 Feb 2025 15:09:43: #2 predicted fragment length is 296 bps INFO @ Mon, 24 Feb 2025 15:09:43: #2 alternative fragment length(s) may be 296 bps INFO @ Mon, 24 Feb 2025 15:09:43: #2.2 Generate R script for model : T1P_HA_hg38_callpeaks1_model.r INFO @ Mon, 24 Feb 2025 15:09:43: #3 Call peaks... INFO @ Mon, 24 Feb 2025 15:09:43: #3 Going to call summits inside each peak ... INFO @ Mon, 24 Feb 2025 15:09:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 24 Feb 2025 15:10:11: #3 In the peak calling step, the following will be performed simultaneously: INFO @ Mon, 24 Feb 2025 15:10:11: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... T1P_HA_hg38_callpeaks1_treat_pileup.bdg INFO @ Mon, 24 Feb 2025 15:10:11: #3 Write bedGraph files for control lambda (after scaling if necessary)... T1P_HA_hg38_callpeaks1_control_lambda.bdg INFO @ Mon, 24 Feb 2025 15:10:11: #3 Pileup will be based on sequencing depth in treatment. INFO @ Mon, 24 Feb 2025 15:10:11: #3 Call peaks for each chromosome... INFO @ Mon, 24 Feb 2025 15:10:39: #4 Write output xls file... T1P_HA_hg38_callpeaks1_peaks.xls INFO @ Mon, 24 Feb 2025 15:10:39: #4 Write peak in narrowPeak format file... T1P_HA_hg38_callpeaks1_peaks.narrowPeak INFO @ Mon, 24 Feb 2025 15:10:39: #4 Write summits bed file... T1P_HA_hg38_callpeaks1_summits.bed INFO @ Mon, 24 Feb 2025 15:10:39: Done! INFO @ Mon, 24 Feb 2025 15:10:39: # Command line: callpeak -t T2P_HA_hg38_sorted.bam -c T2P_IgG_hg38_sorted.bam -f BAM -g hs -n T2P_HA_hg38_callpeaks1 --call-summits -q 0.05 --bdg # ARGUMENTS LIST: # name = T2P_HA_hg38_callpeaks1 # format = BAM # ChIP-seq file = ['T2P_HA_hg38_sorted.bam'] # control file = ['T2P_IgG_hg38_sorted.bam'] # effective genome size = 2.70e+09 # band width = 300 # 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 # Searching for subpeak summits is on INFO @ Mon, 24 Feb 2025 15:10:39: #1 read tag files... INFO @ Mon, 24 Feb 2025 15:10:39: #1 read treatment tags... INFO @ Mon, 24 Feb 2025 15:10:45: 1000000 INFO @ Mon, 24 Feb 2025 15:10:51: 2000000 INFO @ Mon, 24 Feb 2025 15:10:56: 3000000 INFO @ Mon, 24 Feb 2025 15:11:03: 3213360 reads have been read. INFO @ Mon, 24 Feb 2025 15:11:03: #1.2 read input tags... INFO @ Mon, 24 Feb 2025 15:11:08: 1000000 INFO @ Mon, 24 Feb 2025 15:11:14: 2000000 INFO @ Mon, 24 Feb 2025 15:11:19: 3000000 INFO @ Mon, 24 Feb 2025 15:11:24: 4000000 INFO @ Mon, 24 Feb 2025 15:11:30: 5000000 INFO @ Mon, 24 Feb 2025 15:11:42: 5061712 reads have been read. INFO @ Mon, 24 Feb 2025 15:11:42: #1 tag size is determined as 101 bps INFO @ Mon, 24 Feb 2025 15:11:42: #1 tag size = 101.0 INFO @ Mon, 24 Feb 2025 15:11:42: #1 total tags in treatment: 3213360 INFO @ Mon, 24 Feb 2025 15:11:42: #1 user defined the maximum tags... INFO @ Mon, 24 Feb 2025 15:11:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 24 Feb 2025 15:11:42: #1 tags after filtering in treatment: 3134266 INFO @ Mon, 24 Feb 2025 15:11:42: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 24 Feb 2025 15:11:42: #1 total tags in control: 5061712 INFO @ Mon, 24 Feb 2025 15:11:42: #1 user defined the maximum tags... INFO @ Mon, 24 Feb 2025 15:11:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 24 Feb 2025 15:11:42: #1 tags after filtering in control: 4929779 INFO @ Mon, 24 Feb 2025 15:11:42: #1 Redundant rate of control: 0.03 INFO @ Mon, 24 Feb 2025 15:11:42: #1 finished! INFO @ Mon, 24 Feb 2025 15:11:42: #2 Build Peak Model... INFO @ Mon, 24 Feb 2025 15:11:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 24 Feb 2025 15:11:46: #2 number of paired peaks: 29997 INFO @ Mon, 24 Feb 2025 15:11:46: start model_add_line... INFO @ Mon, 24 Feb 2025 15:11:46: start X-correlation... INFO @ Mon, 24 Feb 2025 15:11:46: end of X-cor INFO @ Mon, 24 Feb 2025 15:11:46: #2 finished! INFO @ Mon, 24 Feb 2025 15:11:46: #2 predicted fragment length is 297 bps INFO @ Mon, 24 Feb 2025 15:11:46: #2 alternative fragment length(s) may be 297 bps INFO @ Mon, 24 Feb 2025 15:11:46: #2.2 Generate R script for model : T2P_HA_hg38_callpeaks1_model.r INFO @ Mon, 24 Feb 2025 15:11:46: #3 Call peaks... INFO @ Mon, 24 Feb 2025 15:11:46: #3 Going to call summits inside each peak ... INFO @ Mon, 24 Feb 2025 15:11:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 24 Feb 2025 15:12:06: #3 In the peak calling step, the following will be performed simultaneously: INFO @ Mon, 24 Feb 2025 15:12:06: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... T2P_HA_hg38_callpeaks1_treat_pileup.bdg INFO @ Mon, 24 Feb 2025 15:12:06: #3 Write bedGraph files for control lambda (after scaling if necessary)... T2P_HA_hg38_callpeaks1_control_lambda.bdg INFO @ Mon, 24 Feb 2025 15:12:06: #3 Pileup will be based on sequencing depth in treatment. INFO @ Mon, 24 Feb 2025 15:12:06: #3 Call peaks for each chromosome... INFO @ Mon, 24 Feb 2025 15:12:27: #4 Write output xls file... T2P_HA_hg38_callpeaks1_peaks.xls INFO @ Mon, 24 Feb 2025 15:12:27: #4 Write peak in narrowPeak format file... T2P_HA_hg38_callpeaks1_peaks.narrowPeak INFO @ Mon, 24 Feb 2025 15:12:27: #4 Write summits bed file... T2P_HA_hg38_callpeaks1_summits.bed INFO @ Mon, 24 Feb 2025 15:12:27: Done!