The following have been reloaded with a version change: 1) GCCcore/9.3.0 => GCCcore/8.3.0 2) XZ/5.2.5-GCCcore-9.3.0 => XZ/5.2.4-GCCcore-8.3.0 3) binutils/.2.34-GCCcore-9.3.0 => binutils/.2.32-GCCcore-8.3.0 4) bzip2/1.0.8-GCCcore-9.3.0 => bzip2/1.0.8-GCCcore-8.3.0 5) ncurses/.6.2-GCCcore-9.3.0 => ncurses/.6.1-GCCcore-8.3.0 6) zlib/1.2.11-GCCcore-9.3.0 => zlib/1.2.11-GCCcore-8.3.0 INFO @ Tue, 15 Jun 2021 21:58:28: # Command line: callpeak -t H526_SOX9_S15_R1_001.fastq.gz_bt2_snstv.sorted.rd.bam -c H526_input_S13_R1_001.fastq.gz_bt2_snstv.sorted.rd.bam -g hs -q 0.05 -n H526_SOX9_S15_R1_001.fastq.gz # ARGUMENTS LIST: # name = H526_SOX9_S15_R1_001.fastq.gz # format = AUTO # ChIP-seq file = ['H526_SOX9_S15_R1_001.fastq.gz_bt2_snstv.sorted.rd.bam'] # control file = ['H526_input_S13_R1_001.fastq.gz_bt2_snstv.sorted.rd.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 INFO @ Tue, 15 Jun 2021 21:58:28: #1 read tag files... INFO @ Tue, 15 Jun 2021 21:58:28: #1 read treatment tags... INFO @ Tue, 15 Jun 2021 21:58:28: Detected format is: BAM INFO @ Tue, 15 Jun 2021 21:58:28: * Input file is gzipped. INFO @ Tue, 15 Jun 2021 21:58:31: 1000000 INFO @ Tue, 15 Jun 2021 21:58:34: 2000000 INFO @ Tue, 15 Jun 2021 21:58:37: 3000000 INFO @ Tue, 15 Jun 2021 21:58:40: 4000000 INFO @ Tue, 15 Jun 2021 21:58:42: 5000000 INFO @ Tue, 15 Jun 2021 21:58:46: 6000000 INFO @ Tue, 15 Jun 2021 21:58:49: 7000000 INFO @ Tue, 15 Jun 2021 21:58:52: 8000000 INFO @ Tue, 15 Jun 2021 21:58:55: 9000000 INFO @ Tue, 15 Jun 2021 21:58:58: 10000000 INFO @ Tue, 15 Jun 2021 21:59:00: 11000000 INFO @ Tue, 15 Jun 2021 21:59:04: 12000000 INFO @ Tue, 15 Jun 2021 21:59:07: 13000000 INFO @ Tue, 15 Jun 2021 21:59:10: 14000000 INFO @ Tue, 15 Jun 2021 21:59:13: 15000000 INFO @ Tue, 15 Jun 2021 21:59:16: 16000000 INFO @ Tue, 15 Jun 2021 21:59:19: 17000000 INFO @ Tue, 15 Jun 2021 21:59:28: 17863122 reads have been read. INFO @ Tue, 15 Jun 2021 21:59:28: #1.2 read input tags... INFO @ Tue, 15 Jun 2021 21:59:28: Detected format is: BAM INFO @ Tue, 15 Jun 2021 21:59:28: * Input file is gzipped. INFO @ Tue, 15 Jun 2021 21:59:31: 1000000 INFO @ Tue, 15 Jun 2021 21:59:34: 2000000 INFO @ Tue, 15 Jun 2021 21:59:37: 3000000 INFO @ Tue, 15 Jun 2021 21:59:40: 4000000 INFO @ Tue, 15 Jun 2021 21:59:43: 5000000 INFO @ Tue, 15 Jun 2021 21:59:46: 6000000 INFO @ Tue, 15 Jun 2021 21:59:49: 7000000 INFO @ Tue, 15 Jun 2021 21:59:52: 8000000 INFO @ Tue, 15 Jun 2021 21:59:54: 9000000 INFO @ Tue, 15 Jun 2021 21:59:57: 10000000 INFO @ Tue, 15 Jun 2021 22:00:01: 11000000 INFO @ Tue, 15 Jun 2021 22:00:04: 12000000 INFO @ Tue, 15 Jun 2021 22:00:07: 13000000 INFO @ Tue, 15 Jun 2021 22:00:09: 14000000 INFO @ Tue, 15 Jun 2021 22:00:12: 15000000 INFO @ Tue, 15 Jun 2021 22:00:14: 16000000 INFO @ Tue, 15 Jun 2021 22:00:17: 17000000 INFO @ Tue, 15 Jun 2021 22:00:20: 18000000 INFO @ Tue, 15 Jun 2021 22:00:23: 19000000 INFO @ Tue, 15 Jun 2021 22:00:26: 20000000 INFO @ Tue, 15 Jun 2021 22:00:29: 21000000 INFO @ Tue, 15 Jun 2021 22:00:32: 22000000 INFO @ Tue, 15 Jun 2021 22:00:34: 23000000 INFO @ Tue, 15 Jun 2021 22:00:37: 24000000 INFO @ Tue, 15 Jun 2021 22:00:45: 24660004 reads have been read. INFO @ Tue, 15 Jun 2021 22:00:45: #1 tag size is determined as 76 bps INFO @ Tue, 15 Jun 2021 22:00:45: #1 tag size = 76.0 INFO @ Tue, 15 Jun 2021 22:00:45: #1 total tags in treatment: 17863122 INFO @ Tue, 15 Jun 2021 22:00:45: #1 user defined the maximum tags... INFO @ Tue, 15 Jun 2021 22:00:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 15 Jun 2021 22:00:46: #1 tags after filtering in treatment: 17863112 INFO @ Tue, 15 Jun 2021 22:00:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 15 Jun 2021 22:00:46: #1 total tags in control: 24660004 INFO @ Tue, 15 Jun 2021 22:00:46: #1 user defined the maximum tags... INFO @ Tue, 15 Jun 2021 22:00:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 15 Jun 2021 22:00:46: #1 tags after filtering in control: 24660003 INFO @ Tue, 15 Jun 2021 22:00:46: #1 Redundant rate of control: 0.00 INFO @ Tue, 15 Jun 2021 22:00:46: #1 finished! INFO @ Tue, 15 Jun 2021 22:00:46: #2 Build Peak Model... INFO @ Tue, 15 Jun 2021 22:00:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 15 Jun 2021 22:00:49: #2 number of paired peaks: 15910 INFO @ Tue, 15 Jun 2021 22:00:49: start model_add_line... INFO @ Tue, 15 Jun 2021 22:00:49: start X-correlation... INFO @ Tue, 15 Jun 2021 22:00:49: end of X-cor INFO @ Tue, 15 Jun 2021 22:00:49: #2 finished! INFO @ Tue, 15 Jun 2021 22:00:49: #2 predicted fragment length is 89 bps INFO @ Tue, 15 Jun 2021 22:00:49: #2 alternative fragment length(s) may be 89 bps INFO @ Tue, 15 Jun 2021 22:00:49: #2.2 Generate R script for model : H526_SOX9_S15_R1_001.fastq.gz_model.r WARNING @ Tue, 15 Jun 2021 22:00:49: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 15 Jun 2021 22:00:49: #2 You may need to consider one of the other alternative d(s): 89 WARNING @ Tue, 15 Jun 2021 22:00:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 15 Jun 2021 22:00:49: #3 Call peaks... INFO @ Tue, 15 Jun 2021 22:00:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 15 Jun 2021 22:02:39: #3 Call peaks for each chromosome... INFO @ Tue, 15 Jun 2021 22:03:39: #4 Write output xls file... H526_SOX9_S15_R1_001.fastq.gz_peaks.xls INFO @ Tue, 15 Jun 2021 22:03:39: #4 Write peak in narrowPeak format file... H526_SOX9_S15_R1_001.fastq.gz_peaks.narrowPeak INFO @ Tue, 15 Jun 2021 22:03:39: #4 Write summits bed file... H526_SOX9_S15_R1_001.fastq.gz_summits.bed INFO @ Tue, 15 Jun 2021 22:03:39: Done!