Inactive Modules: 1) slurm INFO @ Mon, 24 Feb 2025 14:55:54: # Command line: callpeak -t T1P_HA_hg38_sorted.bam -c T1P_IgG_hg38_sorted.bam -f BAM -g hs -n T1P_HA_hg38_callpeaks --call-summits -q 0.01 --bdg # ARGUMENTS LIST: # name = T1P_HA_hg38_callpeaks # 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 = 1.00e-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 14:55:54: #1 read tag files... INFO @ Mon, 24 Feb 2025 14:55:54: #1 read treatment tags... INFO @ Mon, 24 Feb 2025 14:55:59: 1000000 INFO @ Mon, 24 Feb 2025 14:56:05: 2000000 INFO @ Mon, 24 Feb 2025 14:56:17: 2880259 reads have been read. INFO @ Mon, 24 Feb 2025 14:56:17: #1.2 read input tags... INFO @ Mon, 24 Feb 2025 14:56:22: 1000000 INFO @ Mon, 24 Feb 2025 14:56:28: 2000000 INFO @ Mon, 24 Feb 2025 14:56:33: 3000000 INFO @ Mon, 24 Feb 2025 14:56:38: 4000000 INFO @ Mon, 24 Feb 2025 14:56:44: 5000000 INFO @ Mon, 24 Feb 2025 14:56:49: 6000000 INFO @ Mon, 24 Feb 2025 14:57:07: 6890662 reads have been read. INFO @ Mon, 24 Feb 2025 14:57:07: #1 tag size is determined as 101 bps INFO @ Mon, 24 Feb 2025 14:57:07: #1 tag size = 101.0 INFO @ Mon, 24 Feb 2025 14:57:07: #1 total tags in treatment: 2880259 INFO @ Mon, 24 Feb 2025 14:57:07: #1 user defined the maximum tags... INFO @ Mon, 24 Feb 2025 14:57:07: #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 14:57:07: #1 tags after filtering in treatment: 2807962 INFO @ Mon, 24 Feb 2025 14:57:07: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 24 Feb 2025 14:57:07: #1 total tags in control: 6890662 INFO @ Mon, 24 Feb 2025 14:57:07: #1 user defined the maximum tags... INFO @ Mon, 24 Feb 2025 14:57:07: #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 14:57:08: #1 tags after filtering in control: 6700819 INFO @ Mon, 24 Feb 2025 14:57:08: #1 Redundant rate of control: 0.03 INFO @ Mon, 24 Feb 2025 14:57:08: #1 finished! INFO @ Mon, 24 Feb 2025 14:57:08: #2 Build Peak Model... INFO @ Mon, 24 Feb 2025 14:57:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 24 Feb 2025 14:57:11: #2 number of paired peaks: 19958 INFO @ Mon, 24 Feb 2025 14:57:11: start model_add_line... INFO @ Mon, 24 Feb 2025 14:57:11: start X-correlation... INFO @ Mon, 24 Feb 2025 14:57:11: end of X-cor INFO @ Mon, 24 Feb 2025 14:57:11: #2 finished! INFO @ Mon, 24 Feb 2025 14:57:11: #2 predicted fragment length is 296 bps INFO @ Mon, 24 Feb 2025 14:57:11: #2 alternative fragment length(s) may be 296 bps INFO @ Mon, 24 Feb 2025 14:57:11: #2.2 Generate R script for model : T1P_HA_hg38_callpeaks_model.r INFO @ Mon, 24 Feb 2025 14:57:11: #3 Call peaks... INFO @ Mon, 24 Feb 2025 14:57:11: #3 Going to call summits inside each peak ... INFO @ Mon, 24 Feb 2025 14:57:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 24 Feb 2025 14:57:38: #3 In the peak calling step, the following will be performed simultaneously: INFO @ Mon, 24 Feb 2025 14:57:38: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... T1P_HA_hg38_callpeaks_treat_pileup.bdg INFO @ Mon, 24 Feb 2025 14:57:38: #3 Write bedGraph files for control lambda (after scaling if necessary)... T1P_HA_hg38_callpeaks_control_lambda.bdg INFO @ Mon, 24 Feb 2025 14:57:38: #3 Pileup will be based on sequencing depth in treatment. INFO @ Mon, 24 Feb 2025 14:57:38: #3 Call peaks for each chromosome... INFO @ Mon, 24 Feb 2025 14:58:05: #4 Write output xls file... T1P_HA_hg38_callpeaks_peaks.xls INFO @ Mon, 24 Feb 2025 14:58:05: #4 Write peak in narrowPeak format file... T1P_HA_hg38_callpeaks_peaks.narrowPeak INFO @ Mon, 24 Feb 2025 14:58:05: #4 Write summits bed file... T1P_HA_hg38_callpeaks_summits.bed INFO @ Mon, 24 Feb 2025 14:58:05: Done! INFO @ Mon, 24 Feb 2025 14:58:06: # Command line: callpeak -t T2P_HA_hg38_sorted.bam -c T2P_IgG_hg38_sorted.bam -f BAM -g hs -n T2P_HA_hg38_callpeaks --call-summits -q 0.01 --bdg # ARGUMENTS LIST: # name = T2P_HA_hg38_callpeaks # 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 = 1.00e-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 14:58:06: #1 read tag files... INFO @ Mon, 24 Feb 2025 14:58:06: #1 read treatment tags... INFO @ Mon, 24 Feb 2025 14:58:12: 1000000 INFO @ Mon, 24 Feb 2025 14:58:18: 2000000 INFO @ Mon, 24 Feb 2025 14:58:24: 3000000 INFO @ Mon, 24 Feb 2025 14:58:31: 3213360 reads have been read. INFO @ Mon, 24 Feb 2025 14:58:31: #1.2 read input tags... INFO @ Mon, 24 Feb 2025 14:58:37: 1000000 INFO @ Mon, 24 Feb 2025 14:58:42: 2000000 INFO @ Mon, 24 Feb 2025 14:58:48: 3000000 INFO @ Mon, 24 Feb 2025 14:58:53: 4000000 INFO @ Mon, 24 Feb 2025 14:58:59: 5000000 INFO @ Mon, 24 Feb 2025 14:59:12: 5061712 reads have been read. INFO @ Mon, 24 Feb 2025 14:59:12: #1 tag size is determined as 101 bps INFO @ Mon, 24 Feb 2025 14:59:12: #1 tag size = 101.0 INFO @ Mon, 24 Feb 2025 14:59:12: #1 total tags in treatment: 3213360 INFO @ Mon, 24 Feb 2025 14:59:12: #1 user defined the maximum tags... INFO @ Mon, 24 Feb 2025 14:59:12: #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 14:59:12: #1 tags after filtering in treatment: 3134266 INFO @ Mon, 24 Feb 2025 14:59:12: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 24 Feb 2025 14:59:12: #1 total tags in control: 5061712 INFO @ Mon, 24 Feb 2025 14:59:12: #1 user defined the maximum tags... INFO @ Mon, 24 Feb 2025 14:59:12: #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 14:59:13: #1 tags after filtering in control: 4929779 INFO @ Mon, 24 Feb 2025 14:59:13: #1 Redundant rate of control: 0.03 INFO @ Mon, 24 Feb 2025 14:59:13: #1 finished! INFO @ Mon, 24 Feb 2025 14:59:13: #2 Build Peak Model... INFO @ Mon, 24 Feb 2025 14:59:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 24 Feb 2025 14:59:16: #2 number of paired peaks: 29997 INFO @ Mon, 24 Feb 2025 14:59:16: start model_add_line... INFO @ Mon, 24 Feb 2025 14:59:17: start X-correlation... INFO @ Mon, 24 Feb 2025 14:59:17: end of X-cor INFO @ Mon, 24 Feb 2025 14:59:17: #2 finished! INFO @ Mon, 24 Feb 2025 14:59:17: #2 predicted fragment length is 297 bps INFO @ Mon, 24 Feb 2025 14:59:17: #2 alternative fragment length(s) may be 297 bps INFO @ Mon, 24 Feb 2025 14:59:17: #2.2 Generate R script for model : T2P_HA_hg38_callpeaks_model.r INFO @ Mon, 24 Feb 2025 14:59:17: #3 Call peaks... INFO @ Mon, 24 Feb 2025 14:59:17: #3 Going to call summits inside each peak ... INFO @ Mon, 24 Feb 2025 14:59:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 24 Feb 2025 14:59:38: #3 In the peak calling step, the following will be performed simultaneously: INFO @ Mon, 24 Feb 2025 14:59:38: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... T2P_HA_hg38_callpeaks_treat_pileup.bdg INFO @ Mon, 24 Feb 2025 14:59:38: #3 Write bedGraph files for control lambda (after scaling if necessary)... T2P_HA_hg38_callpeaks_control_lambda.bdg INFO @ Mon, 24 Feb 2025 14:59:38: #3 Pileup will be based on sequencing depth in treatment. INFO @ Mon, 24 Feb 2025 14:59:38: #3 Call peaks for each chromosome... INFO @ Mon, 24 Feb 2025 14:59:59: #4 Write output xls file... T2P_HA_hg38_callpeaks_peaks.xls INFO @ Mon, 24 Feb 2025 14:59:59: #4 Write peak in narrowPeak format file... T2P_HA_hg38_callpeaks_peaks.narrowPeak INFO @ Mon, 24 Feb 2025 14:59:59: #4 Write summits bed file... T2P_HA_hg38_callpeaks_summits.bed INFO @ Mon, 24 Feb 2025 14:59:59: Done!