Job ID = 6497422 SRX = SRX494834 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:02:56 prefetch.2.10.7: 1) Downloading 'SRR1198366'... 2020-06-25T22:03:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:05:45 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:05:45 prefetch.2.10.7: 1) 'SRR1198366' was downloaded successfully Read 28363255 spots for SRR1198366/SRR1198366.sra Written 28363255 spots for SRR1198366/SRR1198366.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: 00:07:08 28363255 reads; of these: 28363255 (100.00%) were unpaired; of these: 608609 (2.15%) aligned 0 times 22696902 (80.02%) aligned exactly 1 time 5057744 (17.83%) aligned >1 times 97.85% overall alignment rate Time searching: 00:07:09 Overall time: 00:07:09 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] 8988708 / 27754646 = 0.3239 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 07:21:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494834/SRX494834.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494834/SRX494834.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494834/SRX494834.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494834/SRX494834.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 07:21:15: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:21:15: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:21:20: 1000000 INFO @ Fri, 26 Jun 2020 07:21:26: 2000000 INFO @ Fri, 26 Jun 2020 07:21:31: 3000000 INFO @ Fri, 26 Jun 2020 07:21:36: 4000000 INFO @ Fri, 26 Jun 2020 07:21:42: 5000000 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 07:21:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494834/SRX494834.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494834/SRX494834.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494834/SRX494834.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494834/SRX494834.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 07:21:45: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:21:45: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:21:47: 6000000 INFO @ Fri, 26 Jun 2020 07:21:51: 1000000 INFO @ Fri, 26 Jun 2020 07:21:53: 7000000 INFO @ Fri, 26 Jun 2020 07:21:57: 2000000 INFO @ Fri, 26 Jun 2020 07:21:59: 8000000 INFO @ Fri, 26 Jun 2020 07:22:03: 3000000 INFO @ Fri, 26 Jun 2020 07:22:04: 9000000 INFO @ Fri, 26 Jun 2020 07:22:09: 4000000 INFO @ Fri, 26 Jun 2020 07:22:10: 10000000 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 07:22:14: 5000000 INFO @ Fri, 26 Jun 2020 07:22:16: 11000000 INFO @ Fri, 26 Jun 2020 07:22:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494834/SRX494834.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494834/SRX494834.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494834/SRX494834.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494834/SRX494834.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 07:22:18: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:22:18: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:22:20: 6000000 INFO @ Fri, 26 Jun 2020 07:22:22: 12000000 INFO @ Fri, 26 Jun 2020 07:22:24: 1000000 INFO @ Fri, 26 Jun 2020 07:22:26: 7000000 INFO @ Fri, 26 Jun 2020 07:22:27: 13000000 INFO @ Fri, 26 Jun 2020 07:22:30: 2000000 INFO @ Fri, 26 Jun 2020 07:22:32: 8000000 INFO @ Fri, 26 Jun 2020 07:22:33: 14000000 INFO @ Fri, 26 Jun 2020 07:22:36: 3000000 INFO @ Fri, 26 Jun 2020 07:22:38: 9000000 INFO @ Fri, 26 Jun 2020 07:22:39: 15000000 INFO @ Fri, 26 Jun 2020 07:22:42: 4000000 INFO @ Fri, 26 Jun 2020 07:22:44: 10000000 INFO @ Fri, 26 Jun 2020 07:22:45: 16000000 INFO @ Fri, 26 Jun 2020 07:22:48: 5000000 INFO @ Fri, 26 Jun 2020 07:22:50: 11000000 INFO @ Fri, 26 Jun 2020 07:22:51: 17000000 INFO @ Fri, 26 Jun 2020 07:22:54: 6000000 INFO @ Fri, 26 Jun 2020 07:22:56: 12000000 INFO @ Fri, 26 Jun 2020 07:22:57: 18000000 INFO @ Fri, 26 Jun 2020 07:22:59: 7000000 INFO @ Fri, 26 Jun 2020 07:23:02: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:23:02: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:23:02: #1 total tags in treatment: 18765938 INFO @ Fri, 26 Jun 2020 07:23:02: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:23:02: #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 07:23:02: #1 tags after filtering in treatment: 18765938 INFO @ Fri, 26 Jun 2020 07:23:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:23:02: #1 finished! INFO @ Fri, 26 Jun 2020 07:23:02: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:23:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:23:02: 13000000 INFO @ Fri, 26 Jun 2020 07:23:03: #2 number of paired peaks: 307 WARNING @ Fri, 26 Jun 2020 07:23:03: Fewer paired peaks (307) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 307 pairs to build model! INFO @ Fri, 26 Jun 2020 07:23:03: start model_add_line... INFO @ Fri, 26 Jun 2020 07:23:03: start X-correlation... INFO @ Fri, 26 Jun 2020 07:23:03: end of X-cor INFO @ Fri, 26 Jun 2020 07:23:03: #2 finished! INFO @ Fri, 26 Jun 2020 07:23:03: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:23:03: #2 alternative fragment length(s) may be 1,29,43,542 bps INFO @ Fri, 26 Jun 2020 07:23:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494834/SRX494834.05_model.r INFO @ Fri, 26 Jun 2020 07:23:05: 8000000 INFO @ Fri, 26 Jun 2020 07:23:08: 14000000 INFO @ Fri, 26 Jun 2020 07:23:11: 9000000 INFO @ Fri, 26 Jun 2020 07:23:14: 15000000 WARNING @ Fri, 26 Jun 2020 07:23:14: #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 07:23:14: #2 You may need to consider one of the other alternative d(s): 1,29,43,542 WARNING @ Fri, 26 Jun 2020 07:23:14: #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 07:23:14: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:23:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:23:17: 10000000 INFO @ Fri, 26 Jun 2020 07:23:20: 16000000 INFO @ Fri, 26 Jun 2020 07:23:23: 11000000 INFO @ Fri, 26 Jun 2020 07:23:26: 17000000 INFO @ Fri, 26 Jun 2020 07:23:29: 12000000 INFO @ Fri, 26 Jun 2020 07:23:32: 18000000 INFO @ Fri, 26 Jun 2020 07:23:36: 13000000 INFO @ Fri, 26 Jun 2020 07:23:37: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:23:37: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:23:37: #1 total tags in treatment: 18765938 INFO @ Fri, 26 Jun 2020 07:23:37: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:23:37: #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 07:23:38: #1 tags after filtering in treatment: 18765938 INFO @ Fri, 26 Jun 2020 07:23:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:23:38: #1 finished! INFO @ Fri, 26 Jun 2020 07:23:38: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:23:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:23:39: #2 number of paired peaks: 307 WARNING @ Fri, 26 Jun 2020 07:23:39: Fewer paired peaks (307) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 307 pairs to build model! INFO @ Fri, 26 Jun 2020 07:23:39: start model_add_line... INFO @ Fri, 26 Jun 2020 07:23:39: start X-correlation... INFO @ Fri, 26 Jun 2020 07:23:39: end of X-cor INFO @ Fri, 26 Jun 2020 07:23:39: #2 finished! INFO @ Fri, 26 Jun 2020 07:23:39: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:23:39: #2 alternative fragment length(s) may be 1,29,43,542 bps INFO @ Fri, 26 Jun 2020 07:23:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494834/SRX494834.10_model.r WARNING @ Fri, 26 Jun 2020 07:23:39: #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 07:23:39: #2 You may need to consider one of the other alternative d(s): 1,29,43,542 WARNING @ Fri, 26 Jun 2020 07:23:39: #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 07:23:39: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:23:39: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:23:41: 14000000 INFO @ Fri, 26 Jun 2020 07:23:46: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:23:47: 15000000 INFO @ Fri, 26 Jun 2020 07:23:52: 16000000 INFO @ Fri, 26 Jun 2020 07:23:58: 17000000 INFO @ Fri, 26 Jun 2020 07:24:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494834/SRX494834.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:24:03: 18000000 INFO @ Fri, 26 Jun 2020 07:24:08: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:24:08: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:24:08: #1 total tags in treatment: 18765938 INFO @ Fri, 26 Jun 2020 07:24:08: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:24:08: #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 07:24:08: #1 tags after filtering in treatment: 18765938 INFO @ Fri, 26 Jun 2020 07:24:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:24:08: #1 finished! INFO @ Fri, 26 Jun 2020 07:24:08: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:24:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:24:09: #2 number of paired peaks: 307 WARNING @ Fri, 26 Jun 2020 07:24:09: Fewer paired peaks (307) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 307 pairs to build model! INFO @ Fri, 26 Jun 2020 07:24:09: start model_add_line... INFO @ Fri, 26 Jun 2020 07:24:09: start X-correlation... INFO @ Fri, 26 Jun 2020 07:24:09: end of X-cor INFO @ Fri, 26 Jun 2020 07:24:09: #2 finished! INFO @ Fri, 26 Jun 2020 07:24:09: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:24:09: #2 alternative fragment length(s) may be 1,29,43,542 bps INFO @ Fri, 26 Jun 2020 07:24:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494834/SRX494834.20_model.r INFO @ Fri, 26 Jun 2020 07:24:10: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:24:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494834/SRX494834.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:24:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494834/SRX494834.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:24:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494834/SRX494834.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:24:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494834/SRX494834.05_summits.bed INFO @ Fri, 26 Jun 2020 07:24:43: Done! WARNING @ Fri, 26 Jun 2020 07:24:43: #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 07:24:43: #2 You may need to consider one of the other alternative d(s): 1,29,43,542 WARNING @ Fri, 26 Jun 2020 07:24:43: #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 07:24:43: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:24:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:24:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494834/SRX494834.10_summits.bed INFO @ Fri, 26 Jun 2020 07:24:43: Done! BigWig に変換しました。 pass1 - making usageList (0 chroms)pass1 - making usageList (0 chroms): 1 millis : 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184)needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:25:15: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:25:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494834/SRX494834.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:25:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494834/SRX494834.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:25:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494834/SRX494834.20_summits.bed INFO @ Fri, 26 Jun 2020 07:25:35: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling