Inactive Modules: 1) slurm INFO @ Mon, 24 Feb 2025 14:39:13: # Command line: callpeak -t T1P_P2F3_hg38_sorted.bam -c T1P_IgG_hg38_sorted.bam -f BAM -g hs -n T1P_P2F3_hg38_callpeaks --call-summits -q 0.01 --bdg # ARGUMENTS LIST: # name = T1P_P2F3_hg38_callpeaks # format = BAM # ChIP-seq file = ['T1P_P2F3_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 14:39:13: #1 read tag files... INFO @ Mon, 24 Feb 2025 14:39:13: #1 read treatment tags... INFO @ Mon, 24 Feb 2025 14:39:16: 1000000 INFO @ Mon, 24 Feb 2025 14:39:18: 2000000 INFO @ Mon, 24 Feb 2025 14:39:21: 3000000 INFO @ Mon, 24 Feb 2025 14:39:24: 4000000 INFO @ Mon, 24 Feb 2025 14:39:30: 4525503 reads have been read. INFO @ Mon, 24 Feb 2025 14:39:30: #1.2 read input tags... INFO @ Mon, 24 Feb 2025 14:39:35: 1000000 INFO @ Mon, 24 Feb 2025 14:39:41: 2000000 INFO @ Mon, 24 Feb 2025 14:39:47: 3000000 INFO @ Mon, 24 Feb 2025 14:39:52: 4000000 INFO @ Mon, 24 Feb 2025 14:39:58: 5000000 INFO @ Mon, 24 Feb 2025 14:40:03: 6000000 INFO @ Mon, 24 Feb 2025 14:40:21: 6890662 reads have been read. INFO @ Mon, 24 Feb 2025 14:40:21: #1 tag size is determined as 101 bps INFO @ Mon, 24 Feb 2025 14:40:21: #1 tag size = 101.0 INFO @ Mon, 24 Feb 2025 14:40:21: #1 total tags in treatment: 4525503 INFO @ Mon, 24 Feb 2025 14:40:21: #1 user defined the maximum tags... INFO @ Mon, 24 Feb 2025 14:40:21: #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 14:40:21: #1 tags after filtering in treatment: 4354911 INFO @ Mon, 24 Feb 2025 14:40:21: #1 Redundant rate of treatment: 0.04 INFO @ Mon, 24 Feb 2025 14:40:21: #1 total tags in control: 6890662 INFO @ Mon, 24 Feb 2025 14:40:21: #1 user defined the maximum tags... INFO @ Mon, 24 Feb 2025 14:40:21: #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 14:40:21: #1 tags after filtering in control: 6700819 INFO @ Mon, 24 Feb 2025 14:40:21: #1 Redundant rate of control: 0.03 INFO @ Mon, 24 Feb 2025 14:40:21: #1 finished! INFO @ Mon, 24 Feb 2025 14:40:21: #2 Build Peak Model... INFO @ Mon, 24 Feb 2025 14:40:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 24 Feb 2025 14:40:27: #2 number of paired peaks: 103253 INFO @ Mon, 24 Feb 2025 14:40:27: start model_add_line... INFO @ Mon, 24 Feb 2025 14:40:27: start X-correlation... INFO @ Mon, 24 Feb 2025 14:40:27: end of X-cor INFO @ Mon, 24 Feb 2025 14:40:27: #2 finished! INFO @ Mon, 24 Feb 2025 14:40:27: #2 predicted fragment length is 207 bps INFO @ Mon, 24 Feb 2025 14:40:27: #2 alternative fragment length(s) may be 207 bps INFO @ Mon, 24 Feb 2025 14:40:27: #2.2 Generate R script for model : T1P_P2F3_hg38_callpeaks_model.r INFO @ Mon, 24 Feb 2025 14:40:27: #3 Call peaks... INFO @ Mon, 24 Feb 2025 14:40:27: #3 Going to call summits inside each peak ... INFO @ Mon, 24 Feb 2025 14:40:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 24 Feb 2025 14:40:57: #3 In the peak calling step, the following will be performed simultaneously: INFO @ Mon, 24 Feb 2025 14:40:57: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... T1P_P2F3_hg38_callpeaks_treat_pileup.bdg INFO @ Mon, 24 Feb 2025 14:40:57: #3 Write bedGraph files for control lambda (after scaling if necessary)... T1P_P2F3_hg38_callpeaks_control_lambda.bdg INFO @ Mon, 24 Feb 2025 14:40:57: #3 Pileup will be based on sequencing depth in treatment. INFO @ Mon, 24 Feb 2025 14:40:57: #3 Call peaks for each chromosome... INFO @ Mon, 24 Feb 2025 14:41:38: #4 Write output xls file... T1P_P2F3_hg38_callpeaks_peaks.xls INFO @ Mon, 24 Feb 2025 14:41:38: #4 Write peak in narrowPeak format file... T1P_P2F3_hg38_callpeaks_peaks.narrowPeak INFO @ Mon, 24 Feb 2025 14:41:38: #4 Write summits bed file... T1P_P2F3_hg38_callpeaks_summits.bed INFO @ Mon, 24 Feb 2025 14:41:38: Done! INFO @ Mon, 24 Feb 2025 14:41:39: # Command line: callpeak -t T1P_HA_hg38_sorted.bam -c T1P_IgG_hg38_sorted.bam hs -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', 'hs'] # 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 14:41:39: #1 read tag files... INFO @ Mon, 24 Feb 2025 14:41:39: #1 read treatment tags... INFO @ Mon, 24 Feb 2025 14:41:45: 1000000 INFO @ Mon, 24 Feb 2025 14:41:51: 2000000 INFO @ Mon, 24 Feb 2025 14:42:04: 2880259 reads have been read. INFO @ Mon, 24 Feb 2025 14:42:04: #1.2 read input tags... INFO @ Mon, 24 Feb 2025 14:42:10: 1000000 INFO @ Mon, 24 Feb 2025 14:42:16: 2000000 INFO @ Mon, 24 Feb 2025 14:42:22: 3000000 INFO @ Mon, 24 Feb 2025 14:42:28: 4000000 INFO @ Mon, 24 Feb 2025 14:42:33: 5000000 INFO @ Mon, 24 Feb 2025 14:42:39: 6000000 INFO @ Mon, 24 Feb 2025 14:42:59: 6890662 reads have been read. Traceback (most recent call last): File "/grid/it/data/elzar/easybuild/software/Python/3.7.4-GCCcore-8.3.0/bin/macs2", line 653, in main() File "/grid/it/data/elzar/easybuild/software/Python/3.7.4-GCCcore-8.3.0/bin/macs2", line 51, in main run( args ) File "/grid/it/data/elzar/easybuild/software/Python/3.7.4-GCCcore-8.3.0/lib/python3.7/site-packages/MACS2/callpeak_cmd.py", line 65, in run else: (treat, control) = load_tag_files_options (options) File "/grid/it/data/elzar/easybuild/software/Python/3.7.4-GCCcore-8.3.0/lib/python3.7/site-packages/MACS2/callpeak_cmd.py", line 408, in load_tag_files_options cp = options.parser(cfile, buffer_size=options.buffer_size) File "MACS2/IO/Parser.pyx", line 1063, in MACS2.IO.Parser.BAMParser.__init__ File "/grid/it/data/elzar/easybuild/software/Python/3.7.4-GCCcore-8.3.0/lib/python3.7/gzip.py", line 53, in open binary_file = GzipFile(filename, gz_mode, compresslevel) File "/grid/it/data/elzar/easybuild/software/Python/3.7.4-GCCcore-8.3.0/lib/python3.7/gzip.py", line 163, in __init__ fileobj = self.myfileobj = builtins.open(filename, mode or 'rb') FileNotFoundError: [Errno 2] No such file or directory: 'hs' INFO @ Mon, 24 Feb 2025 14:43:00: # Command line: callpeak -t T2P_P2F3_hg38_sorted.bam -c T2P_IgG_hg38_sorted.bam -f BAM -g hs -n T2P_P2F3_hg38_callpeaks --call-summits -q 0.01 --bdg # ARGUMENTS LIST: # name = T2P_P2F3_hg38_callpeaks # format = BAM # ChIP-seq file = ['T2P_P2F3_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 14:43:00: #1 read tag files... INFO @ Mon, 24 Feb 2025 14:43:00: #1 read treatment tags... INFO @ Mon, 24 Feb 2025 14:43:05: 1000000 INFO @ Mon, 24 Feb 2025 14:43:11: 2000000 INFO @ Mon, 24 Feb 2025 14:43:16: 3000000 INFO @ Mon, 24 Feb 2025 14:43:21: 4000000 INFO @ Mon, 24 Feb 2025 14:43:27: 5000000 INFO @ Mon, 24 Feb 2025 14:43:32: 6000000 INFO @ Mon, 24 Feb 2025 14:43:37: 7000000 INFO @ Mon, 24 Feb 2025 14:43:42: 8000000 INFO @ Mon, 24 Feb 2025 14:43:59: 8964048 reads have been read. INFO @ Mon, 24 Feb 2025 14:44:00: #1.2 read input tags... INFO @ Mon, 24 Feb 2025 14:44:05: 1000000 INFO @ Mon, 24 Feb 2025 14:44:10: 2000000 INFO @ Mon, 24 Feb 2025 14:44:15: 3000000 INFO @ Mon, 24 Feb 2025 14:44:20: 4000000 INFO @ Mon, 24 Feb 2025 14:44:25: 5000000 INFO @ Mon, 24 Feb 2025 14:44:37: 5061712 reads have been read. INFO @ Mon, 24 Feb 2025 14:44:37: #1 tag size is determined as 101 bps INFO @ Mon, 24 Feb 2025 14:44:37: #1 tag size = 101.0 INFO @ Mon, 24 Feb 2025 14:44:37: #1 total tags in treatment: 8964048 INFO @ Mon, 24 Feb 2025 14:44:37: #1 user defined the maximum tags... INFO @ Mon, 24 Feb 2025 14:44:37: #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 14:44:37: #1 tags after filtering in treatment: 8604965 INFO @ Mon, 24 Feb 2025 14:44:37: #1 Redundant rate of treatment: 0.04 INFO @ Mon, 24 Feb 2025 14:44:37: #1 total tags in control: 5061712 INFO @ Mon, 24 Feb 2025 14:44:37: #1 user defined the maximum tags... INFO @ Mon, 24 Feb 2025 14:44:37: #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 14:44:37: #1 tags after filtering in control: 4929779 INFO @ Mon, 24 Feb 2025 14:44:37: #1 Redundant rate of control: 0.03 INFO @ Mon, 24 Feb 2025 14:44:37: #1 finished! INFO @ Mon, 24 Feb 2025 14:44:37: #2 Build Peak Model... INFO @ Mon, 24 Feb 2025 14:44:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 24 Feb 2025 14:44:40: #2 number of paired peaks: 46807 INFO @ Mon, 24 Feb 2025 14:44:40: start model_add_line... INFO @ Mon, 24 Feb 2025 14:44:40: start X-correlation... INFO @ Mon, 24 Feb 2025 14:44:40: end of X-cor INFO @ Mon, 24 Feb 2025 14:44:40: #2 finished! INFO @ Mon, 24 Feb 2025 14:44:40: #2 predicted fragment length is 197 bps INFO @ Mon, 24 Feb 2025 14:44:40: #2 alternative fragment length(s) may be 197 bps INFO @ Mon, 24 Feb 2025 14:44:40: #2.2 Generate R script for model : T2P_P2F3_hg38_callpeaks_model.r WARNING @ Mon, 24 Feb 2025 14:44:40: #2 Since the d (197) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 24 Feb 2025 14:44:40: #2 You may need to consider one of the other alternative d(s): 197 WARNING @ Mon, 24 Feb 2025 14:44:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 24 Feb 2025 14:44:40: #3 Call peaks... INFO @ Mon, 24 Feb 2025 14:44:40: #3 Going to call summits inside each peak ... INFO @ Mon, 24 Feb 2025 14:44:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 24 Feb 2025 14:45:05: #3 In the peak calling step, the following will be performed simultaneously: INFO @ Mon, 24 Feb 2025 14:45:05: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... T2P_P2F3_hg38_callpeaks_treat_pileup.bdg INFO @ Mon, 24 Feb 2025 14:45:05: #3 Write bedGraph files for control lambda (after scaling if necessary)... T2P_P2F3_hg38_callpeaks_control_lambda.bdg INFO @ Mon, 24 Feb 2025 14:45:05: #3 Pileup will be based on sequencing depth in control. INFO @ Mon, 24 Feb 2025 14:45:05: #3 Call peaks for each chromosome... INFO @ Mon, 24 Feb 2025 14:45:37: #4 Write output xls file... T2P_P2F3_hg38_callpeaks_peaks.xls INFO @ Mon, 24 Feb 2025 14:45:37: #4 Write peak in narrowPeak format file... T2P_P2F3_hg38_callpeaks_peaks.narrowPeak INFO @ Mon, 24 Feb 2025 14:45:37: #4 Write summits bed file... T2P_P2F3_hg38_callpeaks_summits.bed INFO @ Mon, 24 Feb 2025 14:45:37: Done! INFO @ Mon, 24 Feb 2025 14:45:38: # Command line: callpeak -t T2P_HA_hg38_sorted.bam -c T2P_IgG_hg38_sorted.bam hs -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', 'hs'] # 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 14:45:38: #1 read tag files... INFO @ Mon, 24 Feb 2025 14:45:38: #1 read treatment tags... INFO @ Mon, 24 Feb 2025 14:45:43: 1000000 INFO @ Mon, 24 Feb 2025 14:45:49: 2000000 INFO @ Mon, 24 Feb 2025 14:45:54: 3000000 INFO @ Mon, 24 Feb 2025 14:46:01: 3213360 reads have been read. INFO @ Mon, 24 Feb 2025 14:46:01: #1.2 read input tags... INFO @ Mon, 24 Feb 2025 14:46:06: 1000000 INFO @ Mon, 24 Feb 2025 14:46:11: 2000000 INFO @ Mon, 24 Feb 2025 14:46:16: 3000000 INFO @ Mon, 24 Feb 2025 14:46:21: 4000000 INFO @ Mon, 24 Feb 2025 14:46:26: 5000000 INFO @ Mon, 24 Feb 2025 14:46:38: 5061712 reads have been read. Traceback (most recent call last): File "/grid/it/data/elzar/easybuild/software/Python/3.7.4-GCCcore-8.3.0/bin/macs2", line 653, in main() File "/grid/it/data/elzar/easybuild/software/Python/3.7.4-GCCcore-8.3.0/bin/macs2", line 51, in main run( args ) File "/grid/it/data/elzar/easybuild/software/Python/3.7.4-GCCcore-8.3.0/lib/python3.7/site-packages/MACS2/callpeak_cmd.py", line 65, in run else: (treat, control) = load_tag_files_options (options) File "/grid/it/data/elzar/easybuild/software/Python/3.7.4-GCCcore-8.3.0/lib/python3.7/site-packages/MACS2/callpeak_cmd.py", line 408, in load_tag_files_options cp = options.parser(cfile, buffer_size=options.buffer_size) File "MACS2/IO/Parser.pyx", line 1063, in MACS2.IO.Parser.BAMParser.__init__ File "/grid/it/data/elzar/easybuild/software/Python/3.7.4-GCCcore-8.3.0/lib/python3.7/gzip.py", line 53, in open binary_file = GzipFile(filename, gz_mode, compresslevel) File "/grid/it/data/elzar/easybuild/software/Python/3.7.4-GCCcore-8.3.0/lib/python3.7/gzip.py", line 163, in __init__ fileobj = self.myfileobj = builtins.open(filename, mode or 'rb') FileNotFoundError: [Errno 2] No such file or directory: 'hs'