Inactive Modules: 1) slurm INFO @ Mon, 24 Feb 2025 14:12:23: # Command line: callpeak -t P_P2F3_hg38_sorted.bam -c P_IgG_hg38_sorted.bam -f BAM -g hs -n P_P2F3_hg38_callpeaks --call-summits -q 0.01 --bdg # ARGUMENTS LIST: # name = P_P2F3_hg38_callpeaks # format = BAM # ChIP-seq file = ['P_P2F3_hg38_sorted.bam'] # control file = ['P_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 14:12:23: #1 read tag files... INFO @ Mon, 24 Feb 2025 14:12:23: #1 read treatment tags... INFO @ Mon, 24 Feb 2025 14:12:28: 1000000 INFO @ Mon, 24 Feb 2025 14:12:32: 2000000 INFO @ Mon, 24 Feb 2025 14:12:37: 3000000 INFO @ Mon, 24 Feb 2025 14:12:41: 4000000 INFO @ Mon, 24 Feb 2025 14:12:45: 5000000 INFO @ Mon, 24 Feb 2025 14:12:50: 6000000 INFO @ Mon, 24 Feb 2025 14:12:54: 7000000 INFO @ Mon, 24 Feb 2025 14:12:58: 8000000 INFO @ Mon, 24 Feb 2025 14:13:03: 9000000 INFO @ Mon, 24 Feb 2025 14:13:13: 9961505 reads have been read. INFO @ Mon, 24 Feb 2025 14:13:13: #1.2 read input tags... INFO @ Mon, 24 Feb 2025 14:13:18: 1000000 INFO @ Mon, 24 Feb 2025 14:13:23: 2000000 INFO @ Mon, 24 Feb 2025 14:13:27: 3000000 INFO @ Mon, 24 Feb 2025 14:13:39: 3274389 reads have been read. INFO @ Mon, 24 Feb 2025 14:13:39: #1 tag size is determined as 101 bps INFO @ Mon, 24 Feb 2025 14:13:39: #1 tag size = 101.0 INFO @ Mon, 24 Feb 2025 14:13:39: #1 total tags in treatment: 9961505 INFO @ Mon, 24 Feb 2025 14:13:39: #1 user defined the maximum tags... INFO @ Mon, 24 Feb 2025 14:13:39: #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 14:13:39: #1 tags after filtering in treatment: 9453838 INFO @ Mon, 24 Feb 2025 14:13:39: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 24 Feb 2025 14:13:39: #1 total tags in control: 3274389 INFO @ Mon, 24 Feb 2025 14:13:39: #1 user defined the maximum tags... INFO @ Mon, 24 Feb 2025 14:13:39: #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 14:13:39: #1 tags after filtering in control: 3187310 INFO @ Mon, 24 Feb 2025 14:13:39: #1 Redundant rate of control: 0.03 INFO @ Mon, 24 Feb 2025 14:13:39: #1 finished! INFO @ Mon, 24 Feb 2025 14:13:39: #2 Build Peak Model... INFO @ Mon, 24 Feb 2025 14:13:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 24 Feb 2025 14:13:42: #2 number of paired peaks: 86237 INFO @ Mon, 24 Feb 2025 14:13:42: start model_add_line... INFO @ Mon, 24 Feb 2025 14:13:43: start X-correlation... INFO @ Mon, 24 Feb 2025 14:13:43: end of X-cor INFO @ Mon, 24 Feb 2025 14:13:43: #2 finished! INFO @ Mon, 24 Feb 2025 14:13:43: #2 predicted fragment length is 207 bps INFO @ Mon, 24 Feb 2025 14:13:43: #2 alternative fragment length(s) may be 207 bps INFO @ Mon, 24 Feb 2025 14:13:43: #2.2 Generate R script for model : P_P2F3_hg38_callpeaks_model.r INFO @ Mon, 24 Feb 2025 14:13:43: #3 Call peaks... INFO @ Mon, 24 Feb 2025 14:13:43: #3 Going to call summits inside each peak ... INFO @ Mon, 24 Feb 2025 14:13:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 24 Feb 2025 14:14:01: #3 In the peak calling step, the following will be performed simultaneously: INFO @ Mon, 24 Feb 2025 14:14:01: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... P_P2F3_hg38_callpeaks_treat_pileup.bdg INFO @ Mon, 24 Feb 2025 14:14:01: #3 Write bedGraph files for control lambda (after scaling if necessary)... P_P2F3_hg38_callpeaks_control_lambda.bdg INFO @ Mon, 24 Feb 2025 14:14:01: #3 Pileup will be based on sequencing depth in control. INFO @ Mon, 24 Feb 2025 14:14:01: #3 Call peaks for each chromosome... INFO @ Mon, 24 Feb 2025 14:14:53: #4 Write output xls file... P_P2F3_hg38_callpeaks_peaks.xls INFO @ Mon, 24 Feb 2025 14:14:53: #4 Write peak in narrowPeak format file... P_P2F3_hg38_callpeaks_peaks.narrowPeak INFO @ Mon, 24 Feb 2025 14:14:53: #4 Write summits bed file... P_P2F3_hg38_callpeaks_summits.bed INFO @ Mon, 24 Feb 2025 14:14:53: Done! INFO @ Mon, 24 Feb 2025 14:14:54: # Command line: callpeak -t P_HA_hg38_sorted.bam -c P_IgG_hg38_sorted.bam -f BAM -g hs -n P_HA_hg38_callpeaks --call-summits -q 0.01 --bdg # ARGUMENTS LIST: # name = P_HA_hg38_callpeaks # format = BAM # ChIP-seq file = ['P_HA_hg38_sorted.bam'] # control file = ['P_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 14:14:54: #1 read tag files... INFO @ Mon, 24 Feb 2025 14:14:54: #1 read treatment tags... INFO @ Mon, 24 Feb 2025 14:14:59: 1000000 INFO @ Mon, 24 Feb 2025 14:15:04: 2000000 INFO @ Mon, 24 Feb 2025 14:15:09: 3000000 INFO @ Mon, 24 Feb 2025 14:15:14: 4000000 INFO @ Mon, 24 Feb 2025 14:15:29: 4699450 reads have been read. INFO @ Mon, 24 Feb 2025 14:15:29: #1.2 read input tags... INFO @ Mon, 24 Feb 2025 14:15:34: 1000000 INFO @ Mon, 24 Feb 2025 14:15:39: 2000000 INFO @ Mon, 24 Feb 2025 14:15:43: 3000000 INFO @ Mon, 24 Feb 2025 14:15:56: 3274389 reads have been read. INFO @ Mon, 24 Feb 2025 14:15:56: #1 tag size is determined as 101 bps INFO @ Mon, 24 Feb 2025 14:15:56: #1 tag size = 101.0 INFO @ Mon, 24 Feb 2025 14:15:56: #1 total tags in treatment: 4699450 INFO @ Mon, 24 Feb 2025 14:15:56: #1 user defined the maximum tags... INFO @ Mon, 24 Feb 2025 14:15:56: #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 14:15:56: #1 tags after filtering in treatment: 4567144 INFO @ Mon, 24 Feb 2025 14:15:56: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 24 Feb 2025 14:15:56: #1 total tags in control: 3274389 INFO @ Mon, 24 Feb 2025 14:15:56: #1 user defined the maximum tags... INFO @ Mon, 24 Feb 2025 14:15:56: #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 14:15:56: #1 tags after filtering in control: 3187310 INFO @ Mon, 24 Feb 2025 14:15:56: #1 Redundant rate of control: 0.03 INFO @ Mon, 24 Feb 2025 14:15:56: #1 finished! INFO @ Mon, 24 Feb 2025 14:15:56: #2 Build Peak Model... INFO @ Mon, 24 Feb 2025 14:15:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 24 Feb 2025 14:15:58: #2 number of paired peaks: 7549 INFO @ Mon, 24 Feb 2025 14:15:58: start model_add_line... INFO @ Mon, 24 Feb 2025 14:15:58: start X-correlation... INFO @ Mon, 24 Feb 2025 14:15:58: end of X-cor INFO @ Mon, 24 Feb 2025 14:15:58: #2 finished! INFO @ Mon, 24 Feb 2025 14:15:58: #2 predicted fragment length is 229 bps INFO @ Mon, 24 Feb 2025 14:15:58: #2 alternative fragment length(s) may be 229 bps INFO @ Mon, 24 Feb 2025 14:15:58: #2.2 Generate R script for model : P_HA_hg38_callpeaks_model.r INFO @ Mon, 24 Feb 2025 14:15:58: #3 Call peaks... INFO @ Mon, 24 Feb 2025 14:15:58: #3 Going to call summits inside each peak ... INFO @ Mon, 24 Feb 2025 14:15:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 24 Feb 2025 14:16:12: #3 In the peak calling step, the following will be performed simultaneously: INFO @ Mon, 24 Feb 2025 14:16:12: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... P_HA_hg38_callpeaks_treat_pileup.bdg INFO @ Mon, 24 Feb 2025 14:16:12: #3 Write bedGraph files for control lambda (after scaling if necessary)... P_HA_hg38_callpeaks_control_lambda.bdg INFO @ Mon, 24 Feb 2025 14:16:12: #3 Pileup will be based on sequencing depth in control. INFO @ Mon, 24 Feb 2025 14:16:12: #3 Call peaks for each chromosome... INFO @ Mon, 24 Feb 2025 14:16:29: #4 Write output xls file... P_HA_hg38_callpeaks_peaks.xls INFO @ Mon, 24 Feb 2025 14:16:29: #4 Write peak in narrowPeak format file... P_HA_hg38_callpeaks_peaks.narrowPeak INFO @ Mon, 24 Feb 2025 14:16:29: #4 Write summits bed file... P_HA_hg38_callpeaks_summits.bed INFO @ Mon, 24 Feb 2025 14:16:29: Done! INFO @ Mon, 24 Feb 2025 14:16:29: # Command line: callpeak -t T1P_P2F3_hg38_sorted.bam -c T1P_IgG_hg38_sorted.bam hs -n T1P_P2F3_hg38_callpeaks --call-summits -q 0.01 --bdg # ARGUMENTS LIST: # name = T1P_P2F3_hg38_callpeaks # format = AUTO # ChIP-seq file = ['T1P_P2F3_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 14:16:29: #1 read tag files... INFO @ Mon, 24 Feb 2025 14:16:29: #1 read treatment tags... INFO @ Mon, 24 Feb 2025 14:16:29: Detected format is: BAM INFO @ Mon, 24 Feb 2025 14:16:29: * Input file is gzipped. INFO @ Mon, 24 Feb 2025 14:16:32: 1000000 INFO @ Mon, 24 Feb 2025 14:16:34: 2000000 INFO @ Mon, 24 Feb 2025 14:16:36: 3000000 INFO @ Mon, 24 Feb 2025 14:16:39: 4000000 INFO @ Mon, 24 Feb 2025 14:16:44: 4525503 reads have been read. INFO @ Mon, 24 Feb 2025 14:16:44: #1.2 read input tags... INFO @ Mon, 24 Feb 2025 14:16:44: Detected format is: BAM INFO @ Mon, 24 Feb 2025 14:16:44: * Input file is gzipped. INFO @ Mon, 24 Feb 2025 14:16:49: 1000000 INFO @ Mon, 24 Feb 2025 14:16:54: 2000000 INFO @ Mon, 24 Feb 2025 14:16:58: 3000000 INFO @ Mon, 24 Feb 2025 14:17:03: 4000000 INFO @ Mon, 24 Feb 2025 14:17:08: 5000000 INFO @ Mon, 24 Feb 2025 14:17:12: 6000000 INFO @ Mon, 24 Feb 2025 14:17:28: 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 59, in MACS2.IO.Parser.guess_parser File "MACS2/IO/Parser.pyx", line 71, in MACS2.IO.Parser.guess_parser 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 14:17:29: # Command line: callpeak -t T1P_HA_hg38_sorted.bam -c T1P_IgG_hg38_sorted.bam hs -n T1P_HA_hg38_callpeaks --call-summits -q 0.01 --bdg # ARGUMENTS LIST: # name = T1P_HA_hg38_callpeaks # format = AUTO # 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 14:17:29: #1 read tag files... INFO @ Mon, 24 Feb 2025 14:17:29: #1 read treatment tags... INFO @ Mon, 24 Feb 2025 14:17:29: Detected format is: BAM INFO @ Mon, 24 Feb 2025 14:17:29: * Input file is gzipped. INFO @ Mon, 24 Feb 2025 14:17:34: 1000000 INFO @ Mon, 24 Feb 2025 14:17:39: 2000000 INFO @ Mon, 24 Feb 2025 14:17:50: 2880259 reads have been read. INFO @ Mon, 24 Feb 2025 14:17:50: #1.2 read input tags... INFO @ Mon, 24 Feb 2025 14:17:50: Detected format is: BAM INFO @ Mon, 24 Feb 2025 14:17:50: * Input file is gzipped. INFO @ Mon, 24 Feb 2025 14:17:55: 1000000 INFO @ Mon, 24 Feb 2025 14:18:00: 2000000 INFO @ Mon, 24 Feb 2025 14:18:04: 3000000 INFO @ Mon, 24 Feb 2025 14:18:09: 4000000 INFO @ Mon, 24 Feb 2025 14:18:14: 5000000 INFO @ Mon, 24 Feb 2025 14:18:19: 6000000 INFO @ Mon, 24 Feb 2025 14:18:35: 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 59, in MACS2.IO.Parser.guess_parser File "MACS2/IO/Parser.pyx", line 71, in MACS2.IO.Parser.guess_parser 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 14:18:35: # Command line: callpeak -t T2P_P2F3_hg38_sorted.bam -c T2P_IgG_hg38_sorted.bam hs -n T2P_P2F3_hg38_callpeaks --call-summits -q 0.01 --bdg # ARGUMENTS LIST: # name = T2P_P2F3_hg38_callpeaks # format = AUTO # ChIP-seq file = ['T2P_P2F3_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 14:18:35: #1 read tag files... INFO @ Mon, 24 Feb 2025 14:18:35: #1 read treatment tags... INFO @ Mon, 24 Feb 2025 14:18:36: Detected format is: BAM INFO @ Mon, 24 Feb 2025 14:18:36: * Input file is gzipped. INFO @ Mon, 24 Feb 2025 14:18:40: 1000000 INFO @ Mon, 24 Feb 2025 14:18:45: 2000000 INFO @ Mon, 24 Feb 2025 14:18:50: 3000000 INFO @ Mon, 24 Feb 2025 14:18:54: 4000000 INFO @ Mon, 24 Feb 2025 14:18:59: 5000000 INFO @ Mon, 24 Feb 2025 14:19:03: 6000000 INFO @ Mon, 24 Feb 2025 14:19:08: 7000000 INFO @ Mon, 24 Feb 2025 14:19:13: 8000000 INFO @ Mon, 24 Feb 2025 14:19:27: 8964048 reads have been read. INFO @ Mon, 24 Feb 2025 14:19:27: #1.2 read input tags... INFO @ Mon, 24 Feb 2025 14:19:28: Detected format is: BAM INFO @ Mon, 24 Feb 2025 14:19:28: * Input file is gzipped. INFO @ Mon, 24 Feb 2025 14:19:32: 1000000 INFO @ Mon, 24 Feb 2025 14:19:37: 2000000 INFO @ Mon, 24 Feb 2025 14:19:41: 3000000 INFO @ Mon, 24 Feb 2025 14:19:46: 4000000 INFO @ Mon, 24 Feb 2025 14:19:51: 5000000 INFO @ Mon, 24 Feb 2025 14:20:01: 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 59, in MACS2.IO.Parser.guess_parser File "MACS2/IO/Parser.pyx", line 71, in MACS2.IO.Parser.guess_parser 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 14:20:02: # Command line: callpeak -t T2P_HA_hg38_sorted.bam -c T2P_IgG_hg38_sorted.bam hs -n T2P_HA_hg38_callpeaks --call-summits -q 0.01 --bdg # ARGUMENTS LIST: # name = T2P_HA_hg38_callpeaks # format = AUTO # 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 14:20:02: #1 read tag files... INFO @ Mon, 24 Feb 2025 14:20:02: #1 read treatment tags... INFO @ Mon, 24 Feb 2025 14:20:02: Detected format is: BAM INFO @ Mon, 24 Feb 2025 14:20:02: * Input file is gzipped. INFO @ Mon, 24 Feb 2025 14:20:07: 1000000 INFO @ Mon, 24 Feb 2025 14:20:11: 2000000 INFO @ Mon, 24 Feb 2025 14:20:16: 3000000 INFO @ Mon, 24 Feb 2025 14:20:22: 3213360 reads have been read. INFO @ Mon, 24 Feb 2025 14:20:22: #1.2 read input tags... INFO @ Mon, 24 Feb 2025 14:20:22: Detected format is: BAM INFO @ Mon, 24 Feb 2025 14:20:22: * Input file is gzipped. INFO @ Mon, 24 Feb 2025 14:20:27: 1000000 INFO @ Mon, 24 Feb 2025 14:20:31: 2000000 INFO @ Mon, 24 Feb 2025 14:20:36: 3000000 INFO @ Mon, 24 Feb 2025 14:20:40: 4000000 INFO @ Mon, 24 Feb 2025 14:20:45: 5000000 INFO @ Mon, 24 Feb 2025 14:20:56: 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 59, in MACS2.IO.Parser.guess_parser File "MACS2/IO/Parser.pyx", line 71, in MACS2.IO.Parser.guess_parser 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 14:20:56: # Command line: callpeak -t T2P_H3K27ac_hg38_sorted.bam -c T2P_IgG_hg38_sorted.bam -f BAM -g hs -n T2P_H3K27ac_hg38_callpeaks --broad -q 0.01 --bdg # ARGUMENTS LIST: # name = T2P_H3K27ac_hg38_callpeaks # format = BAM # ChIP-seq file = ['T2P_H3K27ac_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 for narrow/strong regions = 1.00e-02 # qvalue cutoff for broad/weak regions = 1.00e-01 # 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 on # Paired-End mode is off INFO @ Mon, 24 Feb 2025 14:20:56: #1 read tag files... INFO @ Mon, 24 Feb 2025 14:20:56: #1 read treatment tags... INFO @ Mon, 24 Feb 2025 14:21:01: 1000000 INFO @ Mon, 24 Feb 2025 14:21:05: 2000000 INFO @ Mon, 24 Feb 2025 14:21:10: 3000000 INFO @ Mon, 24 Feb 2025 14:21:14: 4000000 INFO @ Mon, 24 Feb 2025 14:21:19: 5000000 INFO @ Mon, 24 Feb 2025 14:21:23: 6000000 INFO @ Mon, 24 Feb 2025 14:21:28: 7000000 INFO @ Mon, 24 Feb 2025 14:21:32: 8000000 INFO @ Mon, 24 Feb 2025 14:21:36: 9000000 INFO @ Mon, 24 Feb 2025 14:21:41: 10000000 INFO @ Mon, 24 Feb 2025 14:21:45: 11000000 INFO @ Mon, 24 Feb 2025 14:21:50: 12000000 INFO @ Mon, 24 Feb 2025 14:21:54: 13000000 INFO @ Mon, 24 Feb 2025 14:21:59: 14000000 INFO @ Mon, 24 Feb 2025 14:22:04: 15000000 INFO @ Mon, 24 Feb 2025 14:22:08: 16000000 INFO @ Mon, 24 Feb 2025 14:22:12: 17000000 INFO @ Mon, 24 Feb 2025 14:22:17: 18000000 INFO @ Mon, 24 Feb 2025 14:22:21: 19000000 INFO @ Mon, 24 Feb 2025 14:22:25: 20000000 INFO @ Mon, 24 Feb 2025 14:22:30: 21000000 INFO @ Mon, 24 Feb 2025 14:22:34: 22000000 INFO @ Mon, 24 Feb 2025 14:22:39: 23000000 INFO @ Mon, 24 Feb 2025 14:22:43: 24000000 INFO @ Mon, 24 Feb 2025 14:22:47: 25000000 INFO @ Mon, 24 Feb 2025 14:22:52: 26000000 INFO @ Mon, 24 Feb 2025 14:23:06: 26428346 reads have been read. INFO @ Mon, 24 Feb 2025 14:23:06: #1.2 read input tags... INFO @ Mon, 24 Feb 2025 14:23:11: 1000000 INFO @ Mon, 24 Feb 2025 14:23:16: 2000000 INFO @ Mon, 24 Feb 2025 14:23:20: 3000000 INFO @ Mon, 24 Feb 2025 14:23:25: 4000000 INFO @ Mon, 24 Feb 2025 14:23:30: 5000000 INFO @ Mon, 24 Feb 2025 14:23:41: 5061712 reads have been read. INFO @ Mon, 24 Feb 2025 14:23:41: #1 tag size is determined as 101 bps INFO @ Mon, 24 Feb 2025 14:23:41: #1 tag size = 101.0 INFO @ Mon, 24 Feb 2025 14:23:41: #1 total tags in treatment: 26428346 INFO @ Mon, 24 Feb 2025 14:23:41: #1 user defined the maximum tags... INFO @ Mon, 24 Feb 2025 14:23:41: #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 14:23:42: #1 tags after filtering in treatment: 24991106 INFO @ Mon, 24 Feb 2025 14:23:42: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 24 Feb 2025 14:23:42: #1 total tags in control: 5061712 INFO @ Mon, 24 Feb 2025 14:23:42: #1 user defined the maximum tags... INFO @ Mon, 24 Feb 2025 14:23:42: #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 14:23:42: #1 tags after filtering in control: 4929779 INFO @ Mon, 24 Feb 2025 14:23:42: #1 Redundant rate of control: 0.03 INFO @ Mon, 24 Feb 2025 14:23:42: #1 finished! INFO @ Mon, 24 Feb 2025 14:23:42: #2 Build Peak Model... INFO @ Mon, 24 Feb 2025 14:23:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 24 Feb 2025 14:23:47: #2 number of paired peaks: 79606 INFO @ Mon, 24 Feb 2025 14:23:47: start model_add_line... INFO @ Mon, 24 Feb 2025 14:23:48: start X-correlation... INFO @ Mon, 24 Feb 2025 14:23:48: end of X-cor INFO @ Mon, 24 Feb 2025 14:23:48: #2 finished! INFO @ Mon, 24 Feb 2025 14:23:48: #2 predicted fragment length is 185 bps INFO @ Mon, 24 Feb 2025 14:23:48: #2 alternative fragment length(s) may be 185,276 bps INFO @ Mon, 24 Feb 2025 14:23:48: #2.2 Generate R script for model : T2P_H3K27ac_hg38_callpeaks_model.r WARNING @ Mon, 24 Feb 2025 14:23:48: #2 Since the d (185) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 24 Feb 2025 14:23:48: #2 You may need to consider one of the other alternative d(s): 185,276 WARNING @ Mon, 24 Feb 2025 14:23:48: #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 14:23:48: #3 Call peaks... INFO @ Mon, 24 Feb 2025 14:23:48: #3 Call broad peaks with given level1 -log10qvalue cutoff and level2: 2.000000, 1.000000... INFO @ Mon, 24 Feb 2025 14:23:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 24 Feb 2025 14:24:25: #3 In the peak calling step, the following will be performed simultaneously: INFO @ Mon, 24 Feb 2025 14:24:25: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... T2P_H3K27ac_hg38_callpeaks_treat_pileup.bdg INFO @ Mon, 24 Feb 2025 14:24:25: #3 Write bedGraph files for control lambda (after scaling if necessary)... T2P_H3K27ac_hg38_callpeaks_control_lambda.bdg INFO @ Mon, 24 Feb 2025 14:24:25: #3 Call peaks for each chromosome... INFO @ Mon, 24 Feb 2025 14:25:11: #4 Write output xls file... T2P_H3K27ac_hg38_callpeaks_peaks.xls INFO @ Mon, 24 Feb 2025 14:25:11: #4 Write broad peak in broadPeak format file... T2P_H3K27ac_hg38_callpeaks_peaks.broadPeak INFO @ Mon, 24 Feb 2025 14:25:11: #4 Write broad peak in bed12/gappedPeak format file... T2P_H3K27ac_hg38_callpeaks_peaks.gappedPeak INFO @ Mon, 24 Feb 2025 14:25:11: Done! INFO @ Mon, 24 Feb 2025 14:25:11: # Command line: callpeak -t T1P_H3K27ac_hg38_sorted.bam -c T1P_IgG_hg38_sorted.bam -f BAM -g hs -n T1P_H3K27ac_hg38_callpeaks --broad -q 0.01 --bdg # ARGUMENTS LIST: # name = T1P_H3K27ac_hg38_callpeaks # format = BAM # ChIP-seq file = ['T1P_H3K27ac_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 for narrow/strong regions = 1.00e-02 # qvalue cutoff for broad/weak regions = 1.00e-01 # 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 on # Paired-End mode is off INFO @ Mon, 24 Feb 2025 14:25:11: #1 read tag files... INFO @ Mon, 24 Feb 2025 14:25:11: #1 read treatment tags... INFO @ Mon, 24 Feb 2025 14:25:16: 1000000 INFO @ Mon, 24 Feb 2025 14:25:20: 2000000 INFO @ Mon, 24 Feb 2025 14:25:25: 3000000 INFO @ Mon, 24 Feb 2025 14:25:29: 4000000 INFO @ Mon, 24 Feb 2025 14:25:34: 5000000 INFO @ Mon, 24 Feb 2025 14:25:38: 6000000 INFO @ Mon, 24 Feb 2025 14:25:42: 7000000 INFO @ Mon, 24 Feb 2025 14:25:47: 8000000 INFO @ Mon, 24 Feb 2025 14:25:51: 9000000 INFO @ Mon, 24 Feb 2025 14:25:56: 10000000 INFO @ Mon, 24 Feb 2025 14:26:00: 11000000 INFO @ Mon, 24 Feb 2025 14:26:04: 12000000 INFO @ Mon, 24 Feb 2025 14:26:09: 13000000 INFO @ Mon, 24 Feb 2025 14:26:13: 14000000 INFO @ Mon, 24 Feb 2025 14:26:17: 15000000 INFO @ Mon, 24 Feb 2025 14:26:22: 16000000 INFO @ Mon, 24 Feb 2025 14:26:26: 17000000 INFO @ Mon, 24 Feb 2025 14:26:30: 18000000 INFO @ Mon, 24 Feb 2025 14:26:35: 19000000 INFO @ Mon, 24 Feb 2025 14:26:39: 20000000 INFO @ Mon, 24 Feb 2025 14:26:43: 21000000 INFO @ Mon, 24 Feb 2025 14:26:48: 22000000 INFO @ Mon, 24 Feb 2025 14:26:52: 23000000 INFO @ Mon, 24 Feb 2025 14:26:56: 24000000 INFO @ Mon, 24 Feb 2025 14:27:01: 25000000 INFO @ Mon, 24 Feb 2025 14:27:05: 26000000 INFO @ Mon, 24 Feb 2025 14:27:10: 27000000 INFO @ Mon, 24 Feb 2025 14:27:25: 27776872 reads have been read. INFO @ Mon, 24 Feb 2025 14:27:25: #1.2 read input tags... INFO @ Mon, 24 Feb 2025 14:27:30: 1000000 INFO @ Mon, 24 Feb 2025 14:27:34: 2000000 INFO @ Mon, 24 Feb 2025 14:27:39: 3000000 INFO @ Mon, 24 Feb 2025 14:27:44: 4000000 INFO @ Mon, 24 Feb 2025 14:27:48: 5000000 INFO @ Mon, 24 Feb 2025 14:27:53: 6000000 INFO @ Mon, 24 Feb 2025 14:28:09: 6890662 reads have been read. INFO @ Mon, 24 Feb 2025 14:28:09: #1 tag size is determined as 101 bps INFO @ Mon, 24 Feb 2025 14:28:09: #1 tag size = 101.0 INFO @ Mon, 24 Feb 2025 14:28:09: #1 total tags in treatment: 27776872 INFO @ Mon, 24 Feb 2025 14:28:09: #1 user defined the maximum tags... INFO @ Mon, 24 Feb 2025 14:28:09: #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 14:28:09: #1 tags after filtering in treatment: 26193270 INFO @ Mon, 24 Feb 2025 14:28:09: #1 Redundant rate of treatment: 0.06 INFO @ Mon, 24 Feb 2025 14:28:09: #1 total tags in control: 6890662 INFO @ Mon, 24 Feb 2025 14:28:09: #1 user defined the maximum tags... INFO @ Mon, 24 Feb 2025 14:28:09: #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 14:28:09: #1 tags after filtering in control: 6700819 INFO @ Mon, 24 Feb 2025 14:28:09: #1 Redundant rate of control: 0.03 INFO @ Mon, 24 Feb 2025 14:28:09: #1 finished! INFO @ Mon, 24 Feb 2025 14:28:09: #2 Build Peak Model... INFO @ Mon, 24 Feb 2025 14:28:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 24 Feb 2025 14:28:14: #2 number of paired peaks: 73293 INFO @ Mon, 24 Feb 2025 14:28:14: start model_add_line... INFO @ Mon, 24 Feb 2025 14:28:16: start X-correlation... INFO @ Mon, 24 Feb 2025 14:28:16: end of X-cor INFO @ Mon, 24 Feb 2025 14:28:16: #2 finished! INFO @ Mon, 24 Feb 2025 14:28:16: #2 predicted fragment length is 189 bps INFO @ Mon, 24 Feb 2025 14:28:16: #2 alternative fragment length(s) may be 189,267 bps INFO @ Mon, 24 Feb 2025 14:28:16: #2.2 Generate R script for model : T1P_H3K27ac_hg38_callpeaks_model.r WARNING @ Mon, 24 Feb 2025 14:28:16: #2 Since the d (189) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 24 Feb 2025 14:28:16: #2 You may need to consider one of the other alternative d(s): 189,267 WARNING @ Mon, 24 Feb 2025 14:28:16: #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 14:28:16: #3 Call peaks... INFO @ Mon, 24 Feb 2025 14:28:16: #3 Call broad peaks with given level1 -log10qvalue cutoff and level2: 2.000000, 1.000000... INFO @ Mon, 24 Feb 2025 14:28:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 24 Feb 2025 14:28:59: #3 In the peak calling step, the following will be performed simultaneously: INFO @ Mon, 24 Feb 2025 14:28:59: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... T1P_H3K27ac_hg38_callpeaks_treat_pileup.bdg INFO @ Mon, 24 Feb 2025 14:28:59: #3 Write bedGraph files for control lambda (after scaling if necessary)... T1P_H3K27ac_hg38_callpeaks_control_lambda.bdg INFO @ Mon, 24 Feb 2025 14:28:59: #3 Call peaks for each chromosome... INFO @ Mon, 24 Feb 2025 14:29:52: #4 Write output xls file... T1P_H3K27ac_hg38_callpeaks_peaks.xls INFO @ Mon, 24 Feb 2025 14:29:52: #4 Write broad peak in broadPeak format file... T1P_H3K27ac_hg38_callpeaks_peaks.broadPeak INFO @ Mon, 24 Feb 2025 14:29:52: #4 Write broad peak in bed12/gappedPeak format file... T1P_H3K27ac_hg38_callpeaks_peaks.gappedPeak INFO @ Mon, 24 Feb 2025 14:29:52: Done! INFO @ Mon, 24 Feb 2025 14:29:53: # Command line: callpeak -t P_H3K27ac_hg38_sorted.bam -c P_IgG_hg38_sorted.bam -f BAM -g hs -n P_H3K27ac_hg38_callpeaks --broad -q 0.01 --bdg # ARGUMENTS LIST: # name = P_H3K27ac_hg38_callpeaks # format = BAM # ChIP-seq file = ['P_H3K27ac_hg38_sorted.bam'] # control file = ['P_IgG_hg38_sorted.bam'] # effective genome size = 2.70e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff for narrow/strong regions = 1.00e-02 # qvalue cutoff for broad/weak regions = 1.00e-01 # 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 on # Paired-End mode is off INFO @ Mon, 24 Feb 2025 14:29:53: #1 read tag files... INFO @ Mon, 24 Feb 2025 14:29:53: #1 read treatment tags... INFO @ Mon, 24 Feb 2025 14:29:57: 1000000 INFO @ Mon, 24 Feb 2025 14:30:02: 2000000 INFO @ Mon, 24 Feb 2025 14:30:06: 3000000 INFO @ Mon, 24 Feb 2025 14:30:10: 4000000 INFO @ Mon, 24 Feb 2025 14:30:15: 5000000 INFO @ Mon, 24 Feb 2025 14:30:19: 6000000 INFO @ Mon, 24 Feb 2025 14:30:23: 7000000 INFO @ Mon, 24 Feb 2025 14:30:27: 8000000 INFO @ Mon, 24 Feb 2025 14:30:32: 9000000 INFO @ Mon, 24 Feb 2025 14:30:36: 10000000 INFO @ Mon, 24 Feb 2025 14:30:40: 11000000 INFO @ Mon, 24 Feb 2025 14:30:44: 12000000 INFO @ Mon, 24 Feb 2025 14:30:49: 13000000 INFO @ Mon, 24 Feb 2025 14:30:53: 14000000 INFO @ Mon, 24 Feb 2025 14:30:57: 15000000 INFO @ Mon, 24 Feb 2025 14:31:01: 16000000 INFO @ Mon, 24 Feb 2025 14:31:06: 17000000 INFO @ Mon, 24 Feb 2025 14:31:10: 18000000 INFO @ Mon, 24 Feb 2025 14:31:18: 18207139 reads have been read. INFO @ Mon, 24 Feb 2025 14:31:18: #1.2 read input tags... INFO @ Mon, 24 Feb 2025 14:31:23: 1000000 INFO @ Mon, 24 Feb 2025 14:31:28: 2000000 INFO @ Mon, 24 Feb 2025 14:31:32: 3000000 INFO @ Mon, 24 Feb 2025 14:31:44: 3274389 reads have been read. INFO @ Mon, 24 Feb 2025 14:31:44: #1 tag size is determined as 101 bps INFO @ Mon, 24 Feb 2025 14:31:44: #1 tag size = 101.0 INFO @ Mon, 24 Feb 2025 14:31:44: #1 total tags in treatment: 18207139 INFO @ Mon, 24 Feb 2025 14:31:44: #1 user defined the maximum tags... INFO @ Mon, 24 Feb 2025 14:31:44: #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 14:31:44: #1 tags after filtering in treatment: 17387391 INFO @ Mon, 24 Feb 2025 14:31:44: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 24 Feb 2025 14:31:44: #1 total tags in control: 3274389 INFO @ Mon, 24 Feb 2025 14:31:44: #1 user defined the maximum tags... INFO @ Mon, 24 Feb 2025 14:31:44: #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 14:31:44: #1 tags after filtering in control: 3187310 INFO @ Mon, 24 Feb 2025 14:31:44: #1 Redundant rate of control: 0.03 INFO @ Mon, 24 Feb 2025 14:31:44: #1 finished! INFO @ Mon, 24 Feb 2025 14:31:44: #2 Build Peak Model... INFO @ Mon, 24 Feb 2025 14:31:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 24 Feb 2025 14:31:48: #2 number of paired peaks: 83520 INFO @ Mon, 24 Feb 2025 14:31:48: start model_add_line... INFO @ Mon, 24 Feb 2025 14:31:49: start X-correlation... INFO @ Mon, 24 Feb 2025 14:31:49: end of X-cor INFO @ Mon, 24 Feb 2025 14:31:49: #2 finished! INFO @ Mon, 24 Feb 2025 14:31:49: #2 predicted fragment length is 287 bps INFO @ Mon, 24 Feb 2025 14:31:49: #2 alternative fragment length(s) may be 287 bps INFO @ Mon, 24 Feb 2025 14:31:49: #2.2 Generate R script for model : P_H3K27ac_hg38_callpeaks_model.r INFO @ Mon, 24 Feb 2025 14:31:49: #3 Call peaks... INFO @ Mon, 24 Feb 2025 14:31:49: #3 Call broad peaks with given level1 -log10qvalue cutoff and level2: 2.000000, 1.000000... INFO @ Mon, 24 Feb 2025 14:31:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 24 Feb 2025 14:32:15: #3 In the peak calling step, the following will be performed simultaneously: INFO @ Mon, 24 Feb 2025 14:32:15: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... P_H3K27ac_hg38_callpeaks_treat_pileup.bdg INFO @ Mon, 24 Feb 2025 14:32:15: #3 Write bedGraph files for control lambda (after scaling if necessary)... P_H3K27ac_hg38_callpeaks_control_lambda.bdg INFO @ Mon, 24 Feb 2025 14:32:15: #3 Call peaks for each chromosome... INFO @ Mon, 24 Feb 2025 14:32:47: #4 Write output xls file... P_H3K27ac_hg38_callpeaks_peaks.xls INFO @ Mon, 24 Feb 2025 14:32:47: #4 Write broad peak in broadPeak format file... P_H3K27ac_hg38_callpeaks_peaks.broadPeak INFO @ Mon, 24 Feb 2025 14:32:47: #4 Write broad peak in bed12/gappedPeak format file... P_H3K27ac_hg38_callpeaks_peaks.gappedPeak INFO @ Mon, 24 Feb 2025 14:32:47: Done!