Job ID = 6497515 SRX = SRX495105 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:20:00 prefetch.2.10.7: 1) Downloading 'SRR1198637'... 2020-06-25T22:20:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:23:50 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:23:50 prefetch.2.10.7: 1) 'SRR1198637' was downloaded successfully Read 32317902 spots for SRR1198637/SRR1198637.sra Written 32317902 spots for SRR1198637/SRR1198637.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: 00:07:30 32317902 reads; of these: 32317902 (100.00%) were unpaired; of these: 1920027 (5.94%) aligned 0 times 24974652 (77.28%) aligned exactly 1 time 5423223 (16.78%) aligned >1 times 94.06% overall alignment rate Time searching: 00:07:30 Overall time: 00:07:30 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 5471660 / 30397875 = 0.1800 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 @ Fri, 26 Jun 2020 07:41:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495105/SRX495105.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495105/SRX495105.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495105/SRX495105.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495105/SRX495105.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Fri, 26 Jun 2020 07:41:13: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:41:13: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:41:19: 1000000 INFO @ Fri, 26 Jun 2020 07:41:25: 2000000 INFO @ Fri, 26 Jun 2020 07:41:31: 3000000 INFO @ Fri, 26 Jun 2020 07:41:37: 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 @ Fri, 26 Jun 2020 07:41:43: 5000000 INFO @ Fri, 26 Jun 2020 07:41:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495105/SRX495105.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495105/SRX495105.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495105/SRX495105.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495105/SRX495105.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Fri, 26 Jun 2020 07:41:43: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:41:43: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:41:49: 6000000 INFO @ Fri, 26 Jun 2020 07:41:50: 1000000 INFO @ Fri, 26 Jun 2020 07:41:55: 7000000 INFO @ Fri, 26 Jun 2020 07:41:56: 2000000 INFO @ Fri, 26 Jun 2020 07:42:02: 8000000 INFO @ Fri, 26 Jun 2020 07:42:03: 3000000 INFO @ Fri, 26 Jun 2020 07:42:08: 9000000 INFO @ Fri, 26 Jun 2020 07:42:09: 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 @ Fri, 26 Jun 2020 07:42:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495105/SRX495105.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495105/SRX495105.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495105/SRX495105.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495105/SRX495105.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Fri, 26 Jun 2020 07:42:13: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:42:13: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:42:15: 10000000 INFO @ Fri, 26 Jun 2020 07:42:15: 5000000 INFO @ Fri, 26 Jun 2020 07:42:20: 1000000 INFO @ Fri, 26 Jun 2020 07:42:21: 11000000 INFO @ Fri, 26 Jun 2020 07:42:22: 6000000 INFO @ Fri, 26 Jun 2020 07:42:26: 2000000 INFO @ Fri, 26 Jun 2020 07:42:27: 12000000 INFO @ Fri, 26 Jun 2020 07:42:28: 7000000 INFO @ Fri, 26 Jun 2020 07:42:33: 3000000 INFO @ Fri, 26 Jun 2020 07:42:34: 13000000 INFO @ Fri, 26 Jun 2020 07:42:35: 8000000 INFO @ Fri, 26 Jun 2020 07:42:39: 4000000 INFO @ Fri, 26 Jun 2020 07:42:40: 14000000 INFO @ Fri, 26 Jun 2020 07:42:41: 9000000 INFO @ Fri, 26 Jun 2020 07:42:46: 5000000 INFO @ Fri, 26 Jun 2020 07:42:47: 15000000 INFO @ Fri, 26 Jun 2020 07:42:48: 10000000 INFO @ Fri, 26 Jun 2020 07:42:52: 6000000 INFO @ Fri, 26 Jun 2020 07:42:53: 16000000 INFO @ Fri, 26 Jun 2020 07:42:54: 11000000 INFO @ Fri, 26 Jun 2020 07:42:58: 7000000 INFO @ Fri, 26 Jun 2020 07:42:59: 17000000 INFO @ Fri, 26 Jun 2020 07:43:00: 12000000 INFO @ Fri, 26 Jun 2020 07:43:05: 8000000 INFO @ Fri, 26 Jun 2020 07:43:06: 18000000 INFO @ Fri, 26 Jun 2020 07:43:07: 13000000 INFO @ Fri, 26 Jun 2020 07:43:11: 9000000 INFO @ Fri, 26 Jun 2020 07:43:12: 19000000 INFO @ Fri, 26 Jun 2020 07:43:13: 14000000 INFO @ Fri, 26 Jun 2020 07:43:18: 10000000 INFO @ Fri, 26 Jun 2020 07:43:19: 20000000 INFO @ Fri, 26 Jun 2020 07:43:20: 15000000 INFO @ Fri, 26 Jun 2020 07:43:24: 11000000 INFO @ Fri, 26 Jun 2020 07:43:25: 21000000 INFO @ Fri, 26 Jun 2020 07:43:26: 16000000 INFO @ Fri, 26 Jun 2020 07:43:31: 12000000 INFO @ Fri, 26 Jun 2020 07:43:31: 22000000 INFO @ Fri, 26 Jun 2020 07:43:33: 17000000 INFO @ Fri, 26 Jun 2020 07:43:37: 13000000 INFO @ Fri, 26 Jun 2020 07:43:38: 23000000 INFO @ Fri, 26 Jun 2020 07:43:39: 18000000 INFO @ Fri, 26 Jun 2020 07:43:44: 14000000 INFO @ Fri, 26 Jun 2020 07:43:44: 24000000 INFO @ Fri, 26 Jun 2020 07:43:46: 19000000 INFO @ Fri, 26 Jun 2020 07:43:50: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:43:50: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:43:50: #1 total tags in treatment: 24926215 INFO @ Fri, 26 Jun 2020 07:43:50: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:43:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:43:50: 15000000 INFO @ Fri, 26 Jun 2020 07:43:50: #1 tags after filtering in treatment: 24926215 INFO @ Fri, 26 Jun 2020 07:43:50: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:43:50: #1 finished! INFO @ Fri, 26 Jun 2020 07:43:50: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:43:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:43:52: #2 number of paired peaks: 134 WARNING @ Fri, 26 Jun 2020 07:43:52: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Fri, 26 Jun 2020 07:43:52: start model_add_line... INFO @ Fri, 26 Jun 2020 07:43:52: 20000000 INFO @ Fri, 26 Jun 2020 07:43:52: start X-correlation... INFO @ Fri, 26 Jun 2020 07:43:52: end of X-cor INFO @ Fri, 26 Jun 2020 07:43:52: #2 finished! INFO @ Fri, 26 Jun 2020 07:43:52: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:43:52: #2 alternative fragment length(s) may be 1,45,211,535 bps INFO @ Fri, 26 Jun 2020 07:43:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495105/SRX495105.05_model.r WARNING @ Fri, 26 Jun 2020 07:43:52: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:43:52: #2 You may need to consider one of the other alternative d(s): 1,45,211,535 WARNING @ Fri, 26 Jun 2020 07:43:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:43:52: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:43:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:43:57: 16000000 INFO @ Fri, 26 Jun 2020 07:43:58: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:44:03: 17000000 INFO @ Fri, 26 Jun 2020 07:44:05: 22000000 INFO @ Fri, 26 Jun 2020 07:44:09: 18000000 INFO @ Fri, 26 Jun 2020 07:44:11: 23000000 INFO @ Fri, 26 Jun 2020 07:44:16: 19000000 INFO @ Fri, 26 Jun 2020 07:44:17: 24000000 INFO @ Fri, 26 Jun 2020 07:44:22: 20000000 INFO @ Fri, 26 Jun 2020 07:44:23: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:44:23: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:44:23: #1 total tags in treatment: 24926215 INFO @ Fri, 26 Jun 2020 07:44:23: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:44:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:44:23: #1 tags after filtering in treatment: 24926215 INFO @ Fri, 26 Jun 2020 07:44:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:44:23: #1 finished! INFO @ Fri, 26 Jun 2020 07:44:23: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:44:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:44:25: #2 number of paired peaks: 134 WARNING @ Fri, 26 Jun 2020 07:44:25: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Fri, 26 Jun 2020 07:44:25: start model_add_line... INFO @ Fri, 26 Jun 2020 07:44:25: start X-correlation... INFO @ Fri, 26 Jun 2020 07:44:25: end of X-cor INFO @ Fri, 26 Jun 2020 07:44:25: #2 finished! INFO @ Fri, 26 Jun 2020 07:44:25: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:44:25: #2 alternative fragment length(s) may be 1,45,211,535 bps INFO @ Fri, 26 Jun 2020 07:44:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495105/SRX495105.10_model.r WARNING @ Fri, 26 Jun 2020 07:44:25: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:44:25: #2 You may need to consider one of the other alternative d(s): 1,45,211,535 WARNING @ Fri, 26 Jun 2020 07:44:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:44:25: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:44:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:44:28: 21000000 INFO @ Fri, 26 Jun 2020 07:44:31: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:44:34: 22000000 INFO @ Fri, 26 Jun 2020 07:44:40: 23000000 INFO @ Fri, 26 Jun 2020 07:44:46: 24000000 INFO @ Fri, 26 Jun 2020 07:44:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495105/SRX495105.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:44:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495105/SRX495105.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:44:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495105/SRX495105.05_summits.bed INFO @ Fri, 26 Jun 2020 07:44:49: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:44:51: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:44:51: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:44:51: #1 total tags in treatment: 24926215 INFO @ Fri, 26 Jun 2020 07:44:51: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:44:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:44:52: #1 tags after filtering in treatment: 24926215 INFO @ Fri, 26 Jun 2020 07:44:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:44:52: #1 finished! INFO @ Fri, 26 Jun 2020 07:44:52: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:44:52: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:44:53: #2 number of paired peaks: 134 WARNING @ Fri, 26 Jun 2020 07:44:53: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Fri, 26 Jun 2020 07:44:53: start model_add_line... INFO @ Fri, 26 Jun 2020 07:44:54: start X-correlation... INFO @ Fri, 26 Jun 2020 07:44:54: end of X-cor INFO @ Fri, 26 Jun 2020 07:44:54: #2 finished! INFO @ Fri, 26 Jun 2020 07:44:54: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:44:54: #2 alternative fragment length(s) may be 1,45,211,535 bps INFO @ Fri, 26 Jun 2020 07:44:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495105/SRX495105.20_model.r WARNING @ Fri, 26 Jun 2020 07:44:54: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:44:54: #2 You may need to consider one of the other alternative d(s): 1,45,211,535 WARNING @ Fri, 26 Jun 2020 07:44:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:44:54: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:44:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:45:03: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:45:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495105/SRX495105.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:45:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495105/SRX495105.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:45:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495105/SRX495105.10_summits.bed INFO @ Fri, 26 Jun 2020 07:45:20: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:45:31: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:45:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495105/SRX495105.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:45:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495105/SRX495105.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:45:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495105/SRX495105.20_summits.bed INFO @ Fri, 26 Jun 2020 07:45:49: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling