Job ID = 14172659 SRX = SRX9427693 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:42 17069370 reads; of these: 17069370 (100.00%) were unpaired; of these: 10972960 (64.28%) aligned 0 times 1390134 (8.14%) aligned exactly 1 time 4706276 (27.57%) aligned >1 times 35.72% overall alignment rate Time searching: 00:03:42 Overall time: 00:03:42 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 2241666 / 6096410 = 0.3677 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 16:31:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9427693/SRX9427693.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9427693/SRX9427693.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9427693/SRX9427693.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9427693/SRX9427693.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 11 Dec 2021 16:31:47: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:31:47: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:31:52: 1000000 INFO @ Sat, 11 Dec 2021 16:31:57: 2000000 INFO @ Sat, 11 Dec 2021 16:32:03: 3000000 INFO @ Sat, 11 Dec 2021 16:32:07: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 16:32:07: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 16:32:07: #1 total tags in treatment: 3854744 INFO @ Sat, 11 Dec 2021 16:32:07: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:32:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 16:32:08: #1 tags after filtering in treatment: 3854703 INFO @ Sat, 11 Dec 2021 16:32:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 16:32:08: #1 finished! INFO @ Sat, 11 Dec 2021 16:32:08: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:32:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:32:08: #2 number of paired peaks: 6737 INFO @ Sat, 11 Dec 2021 16:32:08: start model_add_line... INFO @ Sat, 11 Dec 2021 16:32:08: start X-correlation... INFO @ Sat, 11 Dec 2021 16:32:08: end of X-cor INFO @ Sat, 11 Dec 2021 16:32:08: #2 finished! INFO @ Sat, 11 Dec 2021 16:32:08: #2 predicted fragment length is 56 bps INFO @ Sat, 11 Dec 2021 16:32:08: #2 alternative fragment length(s) may be 4,56 bps INFO @ Sat, 11 Dec 2021 16:32:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9427693/SRX9427693.05_model.r WARNING @ Sat, 11 Dec 2021 16:32:08: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 16:32:08: #2 You may need to consider one of the other alternative d(s): 4,56 WARNING @ Sat, 11 Dec 2021 16:32:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 16:32:08: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:32:08: #3 Pre-compute pvalue-qvalue table... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 16:32:17: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:32:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9427693/SRX9427693.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9427693/SRX9427693.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9427693/SRX9427693.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9427693/SRX9427693.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 11 Dec 2021 16:32:17: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:32:17: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:32:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9427693/SRX9427693.05_peaks.xls INFO @ Sat, 11 Dec 2021 16:32:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9427693/SRX9427693.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:32:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9427693/SRX9427693.05_summits.bed INFO @ Sat, 11 Dec 2021 16:32:21: Done! pass1 - making usageList (1124 chroms): 1 millis pass2 - checking and writing primary data (5196 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 16:32:22: 1000000 INFO @ Sat, 11 Dec 2021 16:32:28: 2000000 INFO @ Sat, 11 Dec 2021 16:32:34: 3000000 INFO @ Sat, 11 Dec 2021 16:32:39: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 16:32:39: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 16:32:39: #1 total tags in treatment: 3854744 INFO @ Sat, 11 Dec 2021 16:32:39: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:32:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 16:32:40: #1 tags after filtering in treatment: 3854703 INFO @ Sat, 11 Dec 2021 16:32:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 16:32:40: #1 finished! INFO @ Sat, 11 Dec 2021 16:32:40: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:32:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:32:40: #2 number of paired peaks: 6737 INFO @ Sat, 11 Dec 2021 16:32:40: start model_add_line... INFO @ Sat, 11 Dec 2021 16:32:40: start X-correlation... INFO @ Sat, 11 Dec 2021 16:32:40: end of X-cor INFO @ Sat, 11 Dec 2021 16:32:40: #2 finished! INFO @ Sat, 11 Dec 2021 16:32:40: #2 predicted fragment length is 56 bps INFO @ Sat, 11 Dec 2021 16:32:40: #2 alternative fragment length(s) may be 4,56 bps INFO @ Sat, 11 Dec 2021 16:32:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9427693/SRX9427693.10_model.r WARNING @ Sat, 11 Dec 2021 16:32:40: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 16:32:40: #2 You may need to consider one of the other alternative d(s): 4,56 WARNING @ Sat, 11 Dec 2021 16:32:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 16:32:40: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:32:40: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 16:32:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9427693/SRX9427693.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9427693/SRX9427693.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9427693/SRX9427693.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9427693/SRX9427693.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 11 Dec 2021 16:32:47: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:32:47: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:32:49: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:32:52: 1000000 INFO @ Sat, 11 Dec 2021 16:32:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9427693/SRX9427693.10_peaks.xls INFO @ Sat, 11 Dec 2021 16:32:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9427693/SRX9427693.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:32:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9427693/SRX9427693.10_summits.bed INFO @ Sat, 11 Dec 2021 16:32:53: Done! pass1 - making usageList (889 chroms): 2 millis pass2 - checking and writing primary data (2837 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 16:32:57: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 16:33:02: 3000000 INFO @ Sat, 11 Dec 2021 16:33:07: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 16:33:07: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 16:33:07: #1 total tags in treatment: 3854744 INFO @ Sat, 11 Dec 2021 16:33:07: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:33:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 16:33:07: #1 tags after filtering in treatment: 3854703 INFO @ Sat, 11 Dec 2021 16:33:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 16:33:07: #1 finished! INFO @ Sat, 11 Dec 2021 16:33:07: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:33:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:33:08: #2 number of paired peaks: 6737 INFO @ Sat, 11 Dec 2021 16:33:08: start model_add_line... INFO @ Sat, 11 Dec 2021 16:33:08: start X-correlation... INFO @ Sat, 11 Dec 2021 16:33:08: end of X-cor INFO @ Sat, 11 Dec 2021 16:33:08: #2 finished! INFO @ Sat, 11 Dec 2021 16:33:08: #2 predicted fragment length is 56 bps INFO @ Sat, 11 Dec 2021 16:33:08: #2 alternative fragment length(s) may be 4,56 bps INFO @ Sat, 11 Dec 2021 16:33:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9427693/SRX9427693.20_model.r WARNING @ Sat, 11 Dec 2021 16:33:08: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 16:33:08: #2 You may need to consider one of the other alternative d(s): 4,56 WARNING @ Sat, 11 Dec 2021 16:33:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 16:33:08: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:33:08: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 16:33:17: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:33:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9427693/SRX9427693.20_peaks.xls INFO @ Sat, 11 Dec 2021 16:33:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9427693/SRX9427693.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:33:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9427693/SRX9427693.20_summits.bed INFO @ Sat, 11 Dec 2021 16:33:21: Done! pass1 - making usageList (480 chroms): 1 millis pass2 - checking and writing primary data (1161 records, 4 fields): 14 millis CompletedMACS2peakCalling