Job ID = 6454134 SRX = SRX1837982 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:15:39 prefetch.2.10.7: 1) Downloading 'SRR3658923'... 2020-06-21T09:15:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:22:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:22:14 prefetch.2.10.7: 1) 'SRR3658923' was downloaded successfully 2020-06-21T09:22:14 prefetch.2.10.7: 'SRR3658923' has 0 unresolved dependencies Read 18924419 spots for SRR3658923/SRR3658923.sra Written 18924419 spots for SRR3658923/SRR3658923.sra 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: 00:18:15 18924419 reads; of these: 18924419 (100.00%) were unpaired; of these: 788586 (4.17%) aligned 0 times 14674146 (77.54%) aligned exactly 1 time 3461687 (18.29%) aligned >1 times 95.83% overall alignment rate Time searching: 00:18:15 Overall time: 00:18:15 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_sort_core] merging from 16 files... [bam_rmdupse_core] 4376929 / 18135833 = 0.2413 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 18:50:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1837982/SRX1837982.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1837982/SRX1837982.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1837982/SRX1837982.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1837982/SRX1837982.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 @ Sun, 21 Jun 2020 18:50:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:50:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:51:07: 1000000 INFO @ Sun, 21 Jun 2020 18:51:16: 2000000 INFO @ Sun, 21 Jun 2020 18:51:25: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 18:51:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1837982/SRX1837982.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1837982/SRX1837982.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1837982/SRX1837982.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1837982/SRX1837982.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 @ Sun, 21 Jun 2020 18:51:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:51:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:51:34: 4000000 INFO @ Sun, 21 Jun 2020 18:51:38: 1000000 INFO @ Sun, 21 Jun 2020 18:51:45: 5000000 INFO @ Sun, 21 Jun 2020 18:51:48: 2000000 INFO @ Sun, 21 Jun 2020 18:51:55: 6000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 18:51:58: 3000000 INFO @ Sun, 21 Jun 2020 18:51:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1837982/SRX1837982.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1837982/SRX1837982.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1837982/SRX1837982.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1837982/SRX1837982.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 @ Sun, 21 Jun 2020 18:51:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:51:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:52:06: 7000000 INFO @ Sun, 21 Jun 2020 18:52:09: 4000000 INFO @ Sun, 21 Jun 2020 18:52:09: 1000000 INFO @ Sun, 21 Jun 2020 18:52:17: 8000000 INFO @ Sun, 21 Jun 2020 18:52:19: 2000000 INFO @ Sun, 21 Jun 2020 18:52:20: 5000000 INFO @ Sun, 21 Jun 2020 18:52:28: 9000000 INFO @ Sun, 21 Jun 2020 18:52:30: 3000000 INFO @ Sun, 21 Jun 2020 18:52:31: 6000000 INFO @ Sun, 21 Jun 2020 18:52:40: 10000000 INFO @ Sun, 21 Jun 2020 18:52:41: 4000000 INFO @ Sun, 21 Jun 2020 18:52:42: 7000000 INFO @ Sun, 21 Jun 2020 18:52:51: 11000000 INFO @ Sun, 21 Jun 2020 18:52:52: 5000000 INFO @ Sun, 21 Jun 2020 18:52:53: 8000000 INFO @ Sun, 21 Jun 2020 18:53:03: 12000000 INFO @ Sun, 21 Jun 2020 18:53:03: 6000000 INFO @ Sun, 21 Jun 2020 18:53:04: 9000000 INFO @ Sun, 21 Jun 2020 18:53:14: 13000000 INFO @ Sun, 21 Jun 2020 18:53:15: 7000000 INFO @ Sun, 21 Jun 2020 18:53:15: 10000000 INFO @ Sun, 21 Jun 2020 18:53:23: #1 tag size is determined as 147 bps INFO @ Sun, 21 Jun 2020 18:53:23: #1 tag size = 147 INFO @ Sun, 21 Jun 2020 18:53:23: #1 total tags in treatment: 13758904 INFO @ Sun, 21 Jun 2020 18:53:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:53:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:53:24: #1 tags after filtering in treatment: 13758720 INFO @ Sun, 21 Jun 2020 18:53:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:53:24: #1 finished! INFO @ Sun, 21 Jun 2020 18:53:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:53:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:53:25: #2 number of paired peaks: 2600 INFO @ Sun, 21 Jun 2020 18:53:25: start model_add_line... INFO @ Sun, 21 Jun 2020 18:53:25: start X-correlation... INFO @ Sun, 21 Jun 2020 18:53:25: end of X-cor INFO @ Sun, 21 Jun 2020 18:53:25: #2 finished! INFO @ Sun, 21 Jun 2020 18:53:25: #2 predicted fragment length is 159 bps INFO @ Sun, 21 Jun 2020 18:53:25: #2 alternative fragment length(s) may be 159 bps INFO @ Sun, 21 Jun 2020 18:53:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1837982/SRX1837982.05_model.r WARNING @ Sun, 21 Jun 2020 18:53:25: #2 Since the d (159) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:53:25: #2 You may need to consider one of the other alternative d(s): 159 WARNING @ Sun, 21 Jun 2020 18:53:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:53:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:53:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:53:25: 8000000 INFO @ Sun, 21 Jun 2020 18:53:26: 11000000 INFO @ Sun, 21 Jun 2020 18:53:35: 9000000 INFO @ Sun, 21 Jun 2020 18:53:36: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:53:44: 10000000 INFO @ Sun, 21 Jun 2020 18:53:46: 13000000 INFO @ Sun, 21 Jun 2020 18:53:53: 11000000 INFO @ Sun, 21 Jun 2020 18:53:54: #1 tag size is determined as 147 bps INFO @ Sun, 21 Jun 2020 18:53:54: #1 tag size = 147 INFO @ Sun, 21 Jun 2020 18:53:54: #1 total tags in treatment: 13758904 INFO @ Sun, 21 Jun 2020 18:53:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:53:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:53:55: #1 tags after filtering in treatment: 13758720 INFO @ Sun, 21 Jun 2020 18:53:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:53:55: #1 finished! INFO @ Sun, 21 Jun 2020 18:53:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:53:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:53:56: #2 number of paired peaks: 2600 INFO @ Sun, 21 Jun 2020 18:53:56: start model_add_line... INFO @ Sun, 21 Jun 2020 18:53:56: start X-correlation... INFO @ Sun, 21 Jun 2020 18:53:56: end of X-cor INFO @ Sun, 21 Jun 2020 18:53:56: #2 finished! INFO @ Sun, 21 Jun 2020 18:53:56: #2 predicted fragment length is 159 bps INFO @ Sun, 21 Jun 2020 18:53:56: #2 alternative fragment length(s) may be 159 bps INFO @ Sun, 21 Jun 2020 18:53:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1837982/SRX1837982.10_model.r WARNING @ Sun, 21 Jun 2020 18:53:56: #2 Since the d (159) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:53:56: #2 You may need to consider one of the other alternative d(s): 159 WARNING @ Sun, 21 Jun 2020 18:53:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:53:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:53:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:53:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:54:03: 12000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:54:11: 13000000 INFO @ Sun, 21 Jun 2020 18:54:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1837982/SRX1837982.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:54:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1837982/SRX1837982.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:54:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1837982/SRX1837982.05_summits.bed INFO @ Sun, 21 Jun 2020 18:54:14: Done! pass1 - making usageList (422 chroms): 6 millis pass2 - checking and writing primary data (30444 records, 4 fields): 56 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:54:18: #1 tag size is determined as 147 bps INFO @ Sun, 21 Jun 2020 18:54:18: #1 tag size = 147 INFO @ Sun, 21 Jun 2020 18:54:18: #1 total tags in treatment: 13758904 INFO @ Sun, 21 Jun 2020 18:54:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:54:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:54:19: #1 tags after filtering in treatment: 13758720 INFO @ Sun, 21 Jun 2020 18:54:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:54:19: #1 finished! INFO @ Sun, 21 Jun 2020 18:54:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:54:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:54:20: #2 number of paired peaks: 2600 INFO @ Sun, 21 Jun 2020 18:54:20: start model_add_line... INFO @ Sun, 21 Jun 2020 18:54:20: start X-correlation... INFO @ Sun, 21 Jun 2020 18:54:20: end of X-cor INFO @ Sun, 21 Jun 2020 18:54:20: #2 finished! INFO @ Sun, 21 Jun 2020 18:54:20: #2 predicted fragment length is 159 bps INFO @ Sun, 21 Jun 2020 18:54:20: #2 alternative fragment length(s) may be 159 bps INFO @ Sun, 21 Jun 2020 18:54:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1837982/SRX1837982.20_model.r WARNING @ Sun, 21 Jun 2020 18:54:20: #2 Since the d (159) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:54:20: #2 You may need to consider one of the other alternative d(s): 159 WARNING @ Sun, 21 Jun 2020 18:54:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:54:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:54:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:54:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:54:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1837982/SRX1837982.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:54:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1837982/SRX1837982.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:54:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1837982/SRX1837982.10_summits.bed INFO @ Sun, 21 Jun 2020 18:54:43: Done! pass1 - making usageList (346 chroms): 4 millis pass2 - checking and writing primary data (20303 records, 4 fields): 41 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:54:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:55:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1837982/SRX1837982.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:55:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1837982/SRX1837982.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:55:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1837982/SRX1837982.20_summits.bed INFO @ Sun, 21 Jun 2020 18:55:07: Done! pass1 - making usageList (255 chroms): 2 millis pass2 - checking and writing primary data (10142 records, 4 fields): 26 millis CompletedMACS2peakCalling