Job ID = 6455194 SRX = SRX2831141 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:42:55 prefetch.2.10.7: 1) Downloading 'SRR5572463'... 2020-06-21T09:42:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:46:10 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:46:10 prefetch.2.10.7: 1) 'SRR5572463' was downloaded successfully Read 31647053 spots for SRR5572463/SRR5572463.sra Written 31647053 spots for SRR5572463/SRR5572463.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:28 31647053 reads; of these: 31647053 (100.00%) were unpaired; of these: 1047606 (3.31%) aligned 0 times 21864089 (69.09%) aligned exactly 1 time 8735358 (27.60%) aligned >1 times 96.69% overall alignment rate Time searching: 00:10:29 Overall time: 00:10:29 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] 4901074 / 30599447 = 0.1602 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 19:05:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2831141/SRX2831141.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2831141/SRX2831141.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2831141/SRX2831141.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2831141/SRX2831141.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 19:05:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:05:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:05:09: 1000000 INFO @ Sun, 21 Jun 2020 19:05:15: 2000000 INFO @ Sun, 21 Jun 2020 19:05:20: 3000000 INFO @ Sun, 21 Jun 2020 19:05:26: 4000000 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 19:05:32: 5000000 INFO @ Sun, 21 Jun 2020 19:05:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2831141/SRX2831141.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2831141/SRX2831141.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2831141/SRX2831141.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2831141/SRX2831141.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 19:05:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:05:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:05:38: 6000000 INFO @ Sun, 21 Jun 2020 19:05:39: 1000000 INFO @ Sun, 21 Jun 2020 19:05:43: 7000000 INFO @ Sun, 21 Jun 2020 19:05:44: 2000000 INFO @ Sun, 21 Jun 2020 19:05:49: 8000000 INFO @ Sun, 21 Jun 2020 19:05:50: 3000000 INFO @ Sun, 21 Jun 2020 19:05:55: 9000000 INFO @ Sun, 21 Jun 2020 19:05:56: 4000000 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 19:06:01: 10000000 INFO @ Sun, 21 Jun 2020 19:06:02: 5000000 INFO @ Sun, 21 Jun 2020 19:06:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2831141/SRX2831141.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2831141/SRX2831141.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2831141/SRX2831141.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2831141/SRX2831141.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 19:06:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:06:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:06:07: 11000000 INFO @ Sun, 21 Jun 2020 19:06:08: 6000000 INFO @ Sun, 21 Jun 2020 19:06:09: 1000000 INFO @ Sun, 21 Jun 2020 19:06:13: 12000000 INFO @ Sun, 21 Jun 2020 19:06:14: 7000000 INFO @ Sun, 21 Jun 2020 19:06:15: 2000000 INFO @ Sun, 21 Jun 2020 19:06:19: 13000000 INFO @ Sun, 21 Jun 2020 19:06:20: 8000000 INFO @ Sun, 21 Jun 2020 19:06:21: 3000000 INFO @ Sun, 21 Jun 2020 19:06:25: 14000000 INFO @ Sun, 21 Jun 2020 19:06:26: 9000000 INFO @ Sun, 21 Jun 2020 19:06:27: 4000000 INFO @ Sun, 21 Jun 2020 19:06:31: 15000000 INFO @ Sun, 21 Jun 2020 19:06:32: 10000000 INFO @ Sun, 21 Jun 2020 19:06:33: 5000000 INFO @ Sun, 21 Jun 2020 19:06:37: 16000000 INFO @ Sun, 21 Jun 2020 19:06:38: 11000000 INFO @ Sun, 21 Jun 2020 19:06:39: 6000000 INFO @ Sun, 21 Jun 2020 19:06:43: 17000000 INFO @ Sun, 21 Jun 2020 19:06:44: 12000000 INFO @ Sun, 21 Jun 2020 19:06:44: 7000000 INFO @ Sun, 21 Jun 2020 19:06:48: 18000000 INFO @ Sun, 21 Jun 2020 19:06:50: 8000000 INFO @ Sun, 21 Jun 2020 19:06:50: 13000000 INFO @ Sun, 21 Jun 2020 19:06:54: 19000000 INFO @ Sun, 21 Jun 2020 19:06:56: 9000000 INFO @ Sun, 21 Jun 2020 19:06:56: 14000000 INFO @ Sun, 21 Jun 2020 19:07:01: 20000000 INFO @ Sun, 21 Jun 2020 19:07:02: 10000000 INFO @ Sun, 21 Jun 2020 19:07:02: 15000000 INFO @ Sun, 21 Jun 2020 19:07:07: 21000000 INFO @ Sun, 21 Jun 2020 19:07:07: 11000000 INFO @ Sun, 21 Jun 2020 19:07:09: 16000000 INFO @ Sun, 21 Jun 2020 19:07:13: 12000000 INFO @ Sun, 21 Jun 2020 19:07:13: 22000000 INFO @ Sun, 21 Jun 2020 19:07:14: 17000000 INFO @ Sun, 21 Jun 2020 19:07:19: 13000000 INFO @ Sun, 21 Jun 2020 19:07:19: 23000000 INFO @ Sun, 21 Jun 2020 19:07:20: 18000000 INFO @ Sun, 21 Jun 2020 19:07:24: 14000000 INFO @ Sun, 21 Jun 2020 19:07:25: 24000000 INFO @ Sun, 21 Jun 2020 19:07:26: 19000000 INFO @ Sun, 21 Jun 2020 19:07:30: 15000000 INFO @ Sun, 21 Jun 2020 19:07:31: 25000000 INFO @ Sun, 21 Jun 2020 19:07:32: 20000000 INFO @ Sun, 21 Jun 2020 19:07:36: 16000000 INFO @ Sun, 21 Jun 2020 19:07:36: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:07:36: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:07:36: #1 total tags in treatment: 25698373 INFO @ Sun, 21 Jun 2020 19:07:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:07:36: #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 19:07:36: #1 tags after filtering in treatment: 25698303 INFO @ Sun, 21 Jun 2020 19:07:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:07:36: #1 finished! INFO @ Sun, 21 Jun 2020 19:07:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:07:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:07:38: #2 number of paired peaks: 1091 INFO @ Sun, 21 Jun 2020 19:07:38: start model_add_line... INFO @ Sun, 21 Jun 2020 19:07:38: start X-correlation... INFO @ Sun, 21 Jun 2020 19:07:38: end of X-cor INFO @ Sun, 21 Jun 2020 19:07:38: #2 finished! INFO @ Sun, 21 Jun 2020 19:07:38: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 19:07:38: #2 alternative fragment length(s) may be 1,20,37,587 bps INFO @ Sun, 21 Jun 2020 19:07:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2831141/SRX2831141.05_model.r WARNING @ Sun, 21 Jun 2020 19:07:38: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:07:38: #2 You may need to consider one of the other alternative d(s): 1,20,37,587 WARNING @ Sun, 21 Jun 2020 19:07:38: #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 19:07:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:07:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:07:38: 21000000 INFO @ Sun, 21 Jun 2020 19:07:41: 17000000 INFO @ Sun, 21 Jun 2020 19:07:45: 22000000 INFO @ Sun, 21 Jun 2020 19:07:47: 18000000 INFO @ Sun, 21 Jun 2020 19:07:50: 23000000 INFO @ Sun, 21 Jun 2020 19:07:52: 19000000 INFO @ Sun, 21 Jun 2020 19:07:56: 24000000 INFO @ Sun, 21 Jun 2020 19:07:58: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:08:02: 25000000 INFO @ Sun, 21 Jun 2020 19:08:04: 21000000 INFO @ Sun, 21 Jun 2020 19:08:06: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:08:06: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:08:06: #1 total tags in treatment: 25698373 INFO @ Sun, 21 Jun 2020 19:08:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:08:06: #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 19:08:07: #1 tags after filtering in treatment: 25698303 INFO @ Sun, 21 Jun 2020 19:08:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:08:07: #1 finished! INFO @ Sun, 21 Jun 2020 19:08:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:08:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:08:08: #2 number of paired peaks: 1091 INFO @ Sun, 21 Jun 2020 19:08:08: start model_add_line... INFO @ Sun, 21 Jun 2020 19:08:09: start X-correlation... INFO @ Sun, 21 Jun 2020 19:08:09: end of X-cor INFO @ Sun, 21 Jun 2020 19:08:09: #2 finished! INFO @ Sun, 21 Jun 2020 19:08:09: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 19:08:09: #2 alternative fragment length(s) may be 1,20,37,587 bps INFO @ Sun, 21 Jun 2020 19:08:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2831141/SRX2831141.10_model.r WARNING @ Sun, 21 Jun 2020 19:08:09: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:08:09: #2 You may need to consider one of the other alternative d(s): 1,20,37,587 WARNING @ Sun, 21 Jun 2020 19:08:09: #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 19:08:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:08:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:08:10: 22000000 INFO @ Sun, 21 Jun 2020 19:08:15: 23000000 INFO @ Sun, 21 Jun 2020 19:08:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:08:21: 24000000 INFO @ Sun, 21 Jun 2020 19:08:27: 25000000 INFO @ Sun, 21 Jun 2020 19:08:31: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:08:31: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:08:31: #1 total tags in treatment: 25698373 INFO @ Sun, 21 Jun 2020 19:08:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:08:31: #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 19:08:31: #1 tags after filtering in treatment: 25698303 INFO @ Sun, 21 Jun 2020 19:08:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:08:31: #1 finished! INFO @ Sun, 21 Jun 2020 19:08:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:08:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:08:33: #2 number of paired peaks: 1091 INFO @ Sun, 21 Jun 2020 19:08:33: start model_add_line... INFO @ Sun, 21 Jun 2020 19:08:33: start X-correlation... INFO @ Sun, 21 Jun 2020 19:08:33: end of X-cor INFO @ Sun, 21 Jun 2020 19:08:33: #2 finished! INFO @ Sun, 21 Jun 2020 19:08:33: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 19:08:33: #2 alternative fragment length(s) may be 1,20,37,587 bps INFO @ Sun, 21 Jun 2020 19:08:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2831141/SRX2831141.20_model.r WARNING @ Sun, 21 Jun 2020 19:08:33: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:08:33: #2 You may need to consider one of the other alternative d(s): 1,20,37,587 WARNING @ Sun, 21 Jun 2020 19:08:33: #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 19:08:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:08:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:08:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2831141/SRX2831141.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:08:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2831141/SRX2831141.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:08:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2831141/SRX2831141.05_summits.bed INFO @ Sun, 21 Jun 2020 19:08:36: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:08:48: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:09:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2831141/SRX2831141.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:09:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2831141/SRX2831141.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:09:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2831141/SRX2831141.10_summits.bed INFO @ Sun, 21 Jun 2020 19:09:08: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:09:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:09:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2831141/SRX2831141.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:09:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2831141/SRX2831141.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:09:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2831141/SRX2831141.20_summits.bed INFO @ Sun, 21 Jun 2020 19:09:34: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling