Job ID = 6497518 SRX = SRX495108 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:54:58 prefetch.2.10.7: 1) Downloading 'SRR1198640'... 2020-06-25T22:54:58 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:57:36 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:57:36 prefetch.2.10.7: 1) 'SRR1198640' was downloaded successfully Read 28380011 spots for SRR1198640/SRR1198640.sra Written 28380011 spots for SRR1198640/SRR1198640.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: 00:06:37 28380011 reads; of these: 28380011 (100.00%) were unpaired; of these: 2425708 (8.55%) aligned 0 times 20667815 (72.83%) aligned exactly 1 time 5286488 (18.63%) aligned >1 times 91.45% overall alignment rate Time searching: 00:06:37 Overall time: 00:06:37 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] 5627240 / 25954303 = 0.2168 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 08:12:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495108/SRX495108.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495108/SRX495108.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495108/SRX495108.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495108/SRX495108.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 08:12:19: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:12:19: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:12:24: 1000000 INFO @ Fri, 26 Jun 2020 08:12:30: 2000000 INFO @ Fri, 26 Jun 2020 08:12:35: 3000000 INFO @ Fri, 26 Jun 2020 08:12:41: 4000000 INFO @ Fri, 26 Jun 2020 08:12:46: 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 08:12:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495108/SRX495108.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495108/SRX495108.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495108/SRX495108.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495108/SRX495108.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 08:12:49: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:12:49: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:12:52: 6000000 INFO @ Fri, 26 Jun 2020 08:12:55: 1000000 INFO @ Fri, 26 Jun 2020 08:12:57: 7000000 INFO @ Fri, 26 Jun 2020 08:13:01: 2000000 INFO @ Fri, 26 Jun 2020 08:13:03: 8000000 INFO @ Fri, 26 Jun 2020 08:13:07: 3000000 INFO @ Fri, 26 Jun 2020 08:13:09: 9000000 INFO @ Fri, 26 Jun 2020 08:13:13: 4000000 INFO @ Fri, 26 Jun 2020 08:13:14: 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 08:13:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495108/SRX495108.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495108/SRX495108.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495108/SRX495108.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495108/SRX495108.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 08:13:19: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:13:19: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:13:20: 5000000 INFO @ Fri, 26 Jun 2020 08:13:20: 11000000 INFO @ Fri, 26 Jun 2020 08:13:25: 1000000 INFO @ Fri, 26 Jun 2020 08:13:26: 12000000 INFO @ Fri, 26 Jun 2020 08:13:26: 6000000 INFO @ Fri, 26 Jun 2020 08:13:31: 2000000 INFO @ Fri, 26 Jun 2020 08:13:31: 13000000 INFO @ Fri, 26 Jun 2020 08:13:32: 7000000 INFO @ Fri, 26 Jun 2020 08:13:37: 14000000 INFO @ Fri, 26 Jun 2020 08:13:37: 3000000 INFO @ Fri, 26 Jun 2020 08:13:38: 8000000 INFO @ Fri, 26 Jun 2020 08:13:42: 15000000 INFO @ Fri, 26 Jun 2020 08:13:43: 4000000 INFO @ Fri, 26 Jun 2020 08:13:45: 9000000 INFO @ Fri, 26 Jun 2020 08:13:48: 16000000 INFO @ Fri, 26 Jun 2020 08:13:49: 5000000 INFO @ Fri, 26 Jun 2020 08:13:51: 10000000 INFO @ Fri, 26 Jun 2020 08:13:53: 17000000 INFO @ Fri, 26 Jun 2020 08:13:55: 6000000 INFO @ Fri, 26 Jun 2020 08:13:57: 11000000 INFO @ Fri, 26 Jun 2020 08:13:59: 18000000 INFO @ Fri, 26 Jun 2020 08:14:01: 7000000 INFO @ Fri, 26 Jun 2020 08:14:03: 12000000 INFO @ Fri, 26 Jun 2020 08:14:04: 19000000 INFO @ Fri, 26 Jun 2020 08:14:06: 8000000 INFO @ Fri, 26 Jun 2020 08:14:09: 13000000 INFO @ Fri, 26 Jun 2020 08:14:10: 20000000 INFO @ Fri, 26 Jun 2020 08:14:12: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:14:12: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:14:12: #1 total tags in treatment: 20327063 INFO @ Fri, 26 Jun 2020 08:14:12: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:14:12: #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 08:14:12: #1 tags after filtering in treatment: 20327063 INFO @ Fri, 26 Jun 2020 08:14:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:14:12: #1 finished! INFO @ Fri, 26 Jun 2020 08:14:12: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:14:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:14:12: 9000000 INFO @ Fri, 26 Jun 2020 08:14:14: #2 number of paired peaks: 253 WARNING @ Fri, 26 Jun 2020 08:14:14: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Fri, 26 Jun 2020 08:14:14: start model_add_line... INFO @ Fri, 26 Jun 2020 08:14:14: start X-correlation... INFO @ Fri, 26 Jun 2020 08:14:14: end of X-cor INFO @ Fri, 26 Jun 2020 08:14:14: #2 finished! INFO @ Fri, 26 Jun 2020 08:14:14: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 08:14:14: #2 alternative fragment length(s) may be 1,33,584 bps INFO @ Fri, 26 Jun 2020 08:14:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495108/SRX495108.05_model.r WARNING @ Fri, 26 Jun 2020 08:14:14: #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 08:14:14: #2 You may need to consider one of the other alternative d(s): 1,33,584 WARNING @ Fri, 26 Jun 2020 08:14:14: #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 08:14:14: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:14:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:14:15: 14000000 INFO @ Fri, 26 Jun 2020 08:14:18: 10000000 INFO @ Fri, 26 Jun 2020 08:14:21: 15000000 INFO @ Fri, 26 Jun 2020 08:14:24: 11000000 INFO @ Fri, 26 Jun 2020 08:14:27: 16000000 INFO @ Fri, 26 Jun 2020 08:14:30: 12000000 INFO @ Fri, 26 Jun 2020 08:14:33: 17000000 INFO @ Fri, 26 Jun 2020 08:14:36: 13000000 INFO @ Fri, 26 Jun 2020 08:14:39: 18000000 INFO @ Fri, 26 Jun 2020 08:14:42: 14000000 INFO @ Fri, 26 Jun 2020 08:14:46: 19000000 INFO @ Fri, 26 Jun 2020 08:14:47: 15000000 INFO @ Fri, 26 Jun 2020 08:14:48: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:14:52: 20000000 INFO @ Fri, 26 Jun 2020 08:14:53: 16000000 INFO @ Fri, 26 Jun 2020 08:14:54: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:14:54: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:14:54: #1 total tags in treatment: 20327063 INFO @ Fri, 26 Jun 2020 08:14:54: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:14:54: #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 08:14:54: #1 tags after filtering in treatment: 20327063 INFO @ Fri, 26 Jun 2020 08:14:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:14:54: #1 finished! INFO @ Fri, 26 Jun 2020 08:14:54: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:14:54: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:14:55: #2 number of paired peaks: 253 WARNING @ Fri, 26 Jun 2020 08:14:55: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Fri, 26 Jun 2020 08:14:55: start model_add_line... INFO @ Fri, 26 Jun 2020 08:14:56: start X-correlation... INFO @ Fri, 26 Jun 2020 08:14:56: end of X-cor INFO @ Fri, 26 Jun 2020 08:14:56: #2 finished! INFO @ Fri, 26 Jun 2020 08:14:56: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 08:14:56: #2 alternative fragment length(s) may be 1,33,584 bps INFO @ Fri, 26 Jun 2020 08:14:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495108/SRX495108.10_model.r WARNING @ Fri, 26 Jun 2020 08:14:58: #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 08:14:58: #2 You may need to consider one of the other alternative d(s): 1,33,584 WARNING @ Fri, 26 Jun 2020 08:14:58: #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 08:14:58: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:14:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:14:59: 17000000 INFO @ Fri, 26 Jun 2020 08:15:04: 18000000 INFO @ Fri, 26 Jun 2020 08:15:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495108/SRX495108.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:15:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495108/SRX495108.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:15:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495108/SRX495108.05_summits.bed INFO @ Fri, 26 Jun 2020 08:15:05: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:15:10: 19000000 INFO @ Fri, 26 Jun 2020 08:15:15: 20000000 INFO @ Fri, 26 Jun 2020 08:15:17: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:15:17: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:15:17: #1 total tags in treatment: 20327063 INFO @ Fri, 26 Jun 2020 08:15:17: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:15:17: #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 08:15:17: #1 tags after filtering in treatment: 20327063 INFO @ Fri, 26 Jun 2020 08:15:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:15:17: #1 finished! INFO @ Fri, 26 Jun 2020 08:15:17: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:15:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:15:18: #2 number of paired peaks: 253 WARNING @ Fri, 26 Jun 2020 08:15:18: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Fri, 26 Jun 2020 08:15:18: start model_add_line... INFO @ Fri, 26 Jun 2020 08:15:19: start X-correlation... INFO @ Fri, 26 Jun 2020 08:15:19: end of X-cor INFO @ Fri, 26 Jun 2020 08:15:19: #2 finished! INFO @ Fri, 26 Jun 2020 08:15:19: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 08:15:19: #2 alternative fragment length(s) may be 1,33,584 bps INFO @ Fri, 26 Jun 2020 08:15:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495108/SRX495108.20_model.r WARNING @ Fri, 26 Jun 2020 08:15:19: #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 08:15:19: #2 You may need to consider one of the other alternative d(s): 1,33,584 WARNING @ Fri, 26 Jun 2020 08:15:19: #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 08:15:19: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:15:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:15:34: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:15:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495108/SRX495108.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:15:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495108/SRX495108.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:15:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495108/SRX495108.10_summits.bed INFO @ Fri, 26 Jun 2020 08:15:50: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:15:54: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:16:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495108/SRX495108.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:16:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495108/SRX495108.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:16:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495108/SRX495108.20_summits.bed INFO @ Fri, 26 Jun 2020 08:16:16: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling