Job ID = 6367236 SRX = SRX3043422 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:24:46 prefetch.2.10.7: 1) Downloading 'SRR5875906'... 2020-06-15T23:24:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:27:31 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:27:31 prefetch.2.10.7: 1) 'SRR5875906' was downloaded successfully 2020-06-15T23:27:31 prefetch.2.10.7: 'SRR5875906' has 0 unresolved dependencies Read 25772598 spots for SRR5875906/SRR5875906.sra Written 25772598 spots for SRR5875906/SRR5875906.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: 00:08:54 25772598 reads; of these: 25772598 (100.00%) were unpaired; of these: 1144779 (4.44%) aligned 0 times 20750533 (80.51%) aligned exactly 1 time 3877286 (15.04%) aligned >1 times 95.56% overall alignment rate Time searching: 00:08:54 Overall time: 00:08:54 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 12 files... [bam_rmdupse_core] 2623227 / 24627819 = 0.1065 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 @ Tue, 16 Jun 2020 08:44:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3043422/SRX3043422.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3043422/SRX3043422.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3043422/SRX3043422.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3043422/SRX3043422.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 @ Tue, 16 Jun 2020 08:44:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:44:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:45:02: 1000000 INFO @ Tue, 16 Jun 2020 08:45:10: 2000000 INFO @ Tue, 16 Jun 2020 08:45:18: 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 @ Tue, 16 Jun 2020 08:45:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3043422/SRX3043422.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3043422/SRX3043422.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3043422/SRX3043422.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3043422/SRX3043422.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 @ Tue, 16 Jun 2020 08:45:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:45:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:45:26: 4000000 INFO @ Tue, 16 Jun 2020 08:45:32: 1000000 INFO @ Tue, 16 Jun 2020 08:45:36: 5000000 INFO @ Tue, 16 Jun 2020 08:45:41: 2000000 INFO @ Tue, 16 Jun 2020 08:45:45: 6000000 INFO @ Tue, 16 Jun 2020 08:45:51: 3000000 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 @ Tue, 16 Jun 2020 08:45:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3043422/SRX3043422.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3043422/SRX3043422.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3043422/SRX3043422.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3043422/SRX3043422.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 @ Tue, 16 Jun 2020 08:45:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:45:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:45:54: 7000000 INFO @ Tue, 16 Jun 2020 08:46:00: 4000000 INFO @ Tue, 16 Jun 2020 08:46:03: 1000000 INFO @ Tue, 16 Jun 2020 08:46:04: 8000000 INFO @ Tue, 16 Jun 2020 08:46:09: 5000000 INFO @ Tue, 16 Jun 2020 08:46:13: 2000000 INFO @ Tue, 16 Jun 2020 08:46:13: 9000000 INFO @ Tue, 16 Jun 2020 08:46:19: 6000000 INFO @ Tue, 16 Jun 2020 08:46:22: 10000000 INFO @ Tue, 16 Jun 2020 08:46:22: 3000000 INFO @ Tue, 16 Jun 2020 08:46:29: 7000000 INFO @ Tue, 16 Jun 2020 08:46:31: 11000000 INFO @ Tue, 16 Jun 2020 08:46:32: 4000000 INFO @ Tue, 16 Jun 2020 08:46:38: 8000000 INFO @ Tue, 16 Jun 2020 08:46:41: 12000000 INFO @ Tue, 16 Jun 2020 08:46:41: 5000000 INFO @ Tue, 16 Jun 2020 08:46:48: 9000000 INFO @ Tue, 16 Jun 2020 08:46:50: 13000000 INFO @ Tue, 16 Jun 2020 08:46:51: 6000000 INFO @ Tue, 16 Jun 2020 08:46:57: 10000000 INFO @ Tue, 16 Jun 2020 08:47:00: 14000000 INFO @ Tue, 16 Jun 2020 08:47:00: 7000000 INFO @ Tue, 16 Jun 2020 08:47:07: 11000000 INFO @ Tue, 16 Jun 2020 08:47:09: 15000000 INFO @ Tue, 16 Jun 2020 08:47:10: 8000000 INFO @ Tue, 16 Jun 2020 08:47:16: 12000000 INFO @ Tue, 16 Jun 2020 08:47:18: 16000000 INFO @ Tue, 16 Jun 2020 08:47:19: 9000000 INFO @ Tue, 16 Jun 2020 08:47:26: 13000000 INFO @ Tue, 16 Jun 2020 08:47:28: 17000000 INFO @ Tue, 16 Jun 2020 08:47:29: 10000000 INFO @ Tue, 16 Jun 2020 08:47:35: 14000000 INFO @ Tue, 16 Jun 2020 08:47:38: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:47:39: 11000000 INFO @ Tue, 16 Jun 2020 08:47:45: 15000000 INFO @ Tue, 16 Jun 2020 08:47:47: 19000000 INFO @ Tue, 16 Jun 2020 08:47:48: 12000000 INFO @ Tue, 16 Jun 2020 08:47:54: 16000000 INFO @ Tue, 16 Jun 2020 08:47:56: 20000000 INFO @ Tue, 16 Jun 2020 08:47:58: 13000000 INFO @ Tue, 16 Jun 2020 08:48:04: 17000000 INFO @ Tue, 16 Jun 2020 08:48:06: 21000000 INFO @ Tue, 16 Jun 2020 08:48:07: 14000000 INFO @ Tue, 16 Jun 2020 08:48:14: 18000000 INFO @ Tue, 16 Jun 2020 08:48:15: 22000000 INFO @ Tue, 16 Jun 2020 08:48:15: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 08:48:15: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 08:48:15: #1 total tags in treatment: 22004592 INFO @ Tue, 16 Jun 2020 08:48:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:48:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:48:16: #1 tags after filtering in treatment: 22004592 INFO @ Tue, 16 Jun 2020 08:48:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:48:16: #1 finished! INFO @ Tue, 16 Jun 2020 08:48:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:48:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:48:17: 15000000 INFO @ Tue, 16 Jun 2020 08:48:17: #2 number of paired peaks: 158 WARNING @ Tue, 16 Jun 2020 08:48:17: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Tue, 16 Jun 2020 08:48:17: start model_add_line... INFO @ Tue, 16 Jun 2020 08:48:17: start X-correlation... INFO @ Tue, 16 Jun 2020 08:48:17: end of X-cor INFO @ Tue, 16 Jun 2020 08:48:17: #2 finished! INFO @ Tue, 16 Jun 2020 08:48:17: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:48:17: #2 alternative fragment length(s) may be 1,26,42,588,592 bps INFO @ Tue, 16 Jun 2020 08:48:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3043422/SRX3043422.05_model.r WARNING @ Tue, 16 Jun 2020 08:48:17: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:48:17: #2 You may need to consider one of the other alternative d(s): 1,26,42,588,592 WARNING @ Tue, 16 Jun 2020 08:48:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:48:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:48:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:48:23: 19000000 INFO @ Tue, 16 Jun 2020 08:48:26: 16000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:48:31: 20000000 INFO @ Tue, 16 Jun 2020 08:48:35: 17000000 INFO @ Tue, 16 Jun 2020 08:48:40: 21000000 INFO @ Tue, 16 Jun 2020 08:48:44: 18000000 INFO @ Tue, 16 Jun 2020 08:48:49: 22000000 INFO @ Tue, 16 Jun 2020 08:48:49: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 08:48:49: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 08:48:49: #1 total tags in treatment: 22004592 INFO @ Tue, 16 Jun 2020 08:48:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:48:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:48:49: #1 tags after filtering in treatment: 22004592 INFO @ Tue, 16 Jun 2020 08:48:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:48:49: #1 finished! INFO @ Tue, 16 Jun 2020 08:48:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:48:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:48:51: #2 number of paired peaks: 158 WARNING @ Tue, 16 Jun 2020 08:48:51: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Tue, 16 Jun 2020 08:48:51: start model_add_line... INFO @ Tue, 16 Jun 2020 08:48:51: start X-correlation... INFO @ Tue, 16 Jun 2020 08:48:51: end of X-cor INFO @ Tue, 16 Jun 2020 08:48:51: #2 finished! INFO @ Tue, 16 Jun 2020 08:48:51: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:48:51: #2 alternative fragment length(s) may be 1,26,42,588,592 bps INFO @ Tue, 16 Jun 2020 08:48:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3043422/SRX3043422.10_model.r WARNING @ Tue, 16 Jun 2020 08:48:51: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:48:51: #2 You may need to consider one of the other alternative d(s): 1,26,42,588,592 WARNING @ Tue, 16 Jun 2020 08:48:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:48:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:48:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:48:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:48:52: 19000000 INFO @ Tue, 16 Jun 2020 08:49:01: 20000000 INFO @ Tue, 16 Jun 2020 08:49:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3043422/SRX3043422.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:49:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3043422/SRX3043422.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:49:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3043422/SRX3043422.05_summits.bed INFO @ Tue, 16 Jun 2020 08:49:09: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:49:09: 21000000 INFO @ Tue, 16 Jun 2020 08:49:17: 22000000 INFO @ Tue, 16 Jun 2020 08:49:17: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 08:49:17: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 08:49:17: #1 total tags in treatment: 22004592 INFO @ Tue, 16 Jun 2020 08:49:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:49:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:49:18: #1 tags after filtering in treatment: 22004592 INFO @ Tue, 16 Jun 2020 08:49:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:49:18: #1 finished! INFO @ Tue, 16 Jun 2020 08:49:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:49:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:49:19: #2 number of paired peaks: 158 WARNING @ Tue, 16 Jun 2020 08:49:19: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Tue, 16 Jun 2020 08:49:19: start model_add_line... INFO @ Tue, 16 Jun 2020 08:49:19: start X-correlation... INFO @ Tue, 16 Jun 2020 08:49:20: end of X-cor INFO @ Tue, 16 Jun 2020 08:49:20: #2 finished! INFO @ Tue, 16 Jun 2020 08:49:20: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:49:20: #2 alternative fragment length(s) may be 1,26,42,588,592 bps INFO @ Tue, 16 Jun 2020 08:49:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3043422/SRX3043422.20_model.r WARNING @ Tue, 16 Jun 2020 08:49:20: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:49:20: #2 You may need to consider one of the other alternative d(s): 1,26,42,588,592 WARNING @ Tue, 16 Jun 2020 08:49:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:49:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:49:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:49:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:49:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3043422/SRX3043422.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:49:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3043422/SRX3043422.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:49:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3043422/SRX3043422.10_summits.bed INFO @ Tue, 16 Jun 2020 08:49:44: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:49:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:50:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3043422/SRX3043422.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:50:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3043422/SRX3043422.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:50:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3043422/SRX3043422.20_summits.bed INFO @ Tue, 16 Jun 2020 08:50:12: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling