Job ID = 6368671 SRX = SRX5402698 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:23:51 prefetch.2.10.7: 1) Downloading 'SRR8602932'... 2020-06-16T00:23:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:28:27 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:28:27 prefetch.2.10.7: 1) 'SRR8602932' was downloaded successfully Read 25974752 spots for SRR8602932/SRR8602932.sra Written 25974752 spots for SRR8602932/SRR8602932.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: 00:05:30 25974752 reads; of these: 25974752 (100.00%) were unpaired; of these: 2609277 (10.05%) aligned 0 times 17719775 (68.22%) aligned exactly 1 time 5645700 (21.74%) aligned >1 times 89.95% overall alignment rate Time searching: 00:05:30 Overall time: 00:05:30 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 12 files... [bam_rmdupse_core] 6139890 / 23365475 = 0.2628 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 09:40:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402698/SRX5402698.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402698/SRX5402698.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402698/SRX5402698.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402698/SRX5402698.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 09:40:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:40:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:40:55: 1000000 INFO @ Tue, 16 Jun 2020 09:41:01: 2000000 INFO @ Tue, 16 Jun 2020 09:41:06: 3000000 INFO @ Tue, 16 Jun 2020 09:41:12: 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 @ Tue, 16 Jun 2020 09:41:18: 5000000 INFO @ Tue, 16 Jun 2020 09:41:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402698/SRX5402698.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402698/SRX5402698.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402698/SRX5402698.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402698/SRX5402698.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 09:41:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:41:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:41:24: 6000000 INFO @ Tue, 16 Jun 2020 09:41:25: 1000000 INFO @ Tue, 16 Jun 2020 09:41:31: 7000000 INFO @ Tue, 16 Jun 2020 09:41:32: 2000000 INFO @ Tue, 16 Jun 2020 09:41:37: 8000000 INFO @ Tue, 16 Jun 2020 09:41:38: 3000000 INFO @ Tue, 16 Jun 2020 09:41:44: 9000000 INFO @ Tue, 16 Jun 2020 09:41:45: 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 @ Tue, 16 Jun 2020 09:41:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402698/SRX5402698.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402698/SRX5402698.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402698/SRX5402698.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402698/SRX5402698.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 09:41:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:41:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:41:50: 10000000 INFO @ Tue, 16 Jun 2020 09:41:51: 5000000 INFO @ Tue, 16 Jun 2020 09:41:56: 1000000 INFO @ Tue, 16 Jun 2020 09:41:57: 11000000 INFO @ Tue, 16 Jun 2020 09:41:58: 6000000 INFO @ Tue, 16 Jun 2020 09:42:03: 2000000 INFO @ Tue, 16 Jun 2020 09:42:04: 12000000 INFO @ Tue, 16 Jun 2020 09:42:05: 7000000 INFO @ Tue, 16 Jun 2020 09:42:10: 3000000 INFO @ Tue, 16 Jun 2020 09:42:11: 13000000 INFO @ Tue, 16 Jun 2020 09:42:12: 8000000 INFO @ Tue, 16 Jun 2020 09:42:17: 4000000 INFO @ Tue, 16 Jun 2020 09:42:18: 14000000 INFO @ Tue, 16 Jun 2020 09:42:19: 9000000 INFO @ Tue, 16 Jun 2020 09:42:23: 5000000 INFO @ Tue, 16 Jun 2020 09:42:25: 15000000 INFO @ Tue, 16 Jun 2020 09:42:26: 10000000 INFO @ Tue, 16 Jun 2020 09:42:30: 6000000 INFO @ Tue, 16 Jun 2020 09:42:31: 16000000 INFO @ Tue, 16 Jun 2020 09:42:33: 11000000 INFO @ Tue, 16 Jun 2020 09:42:37: 7000000 INFO @ Tue, 16 Jun 2020 09:42:38: 17000000 INFO @ Tue, 16 Jun 2020 09:42:39: 12000000 INFO @ Tue, 16 Jun 2020 09:42:40: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:42:40: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:42:40: #1 total tags in treatment: 17225585 INFO @ Tue, 16 Jun 2020 09:42:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:42:40: #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 09:42:40: #1 tags after filtering in treatment: 17225585 INFO @ Tue, 16 Jun 2020 09:42:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:42:40: #1 finished! INFO @ Tue, 16 Jun 2020 09:42:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:42:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:42:41: #2 number of paired peaks: 397 WARNING @ Tue, 16 Jun 2020 09:42:41: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Tue, 16 Jun 2020 09:42:41: start model_add_line... INFO @ Tue, 16 Jun 2020 09:42:41: start X-correlation... INFO @ Tue, 16 Jun 2020 09:42:41: end of X-cor INFO @ Tue, 16 Jun 2020 09:42:41: #2 finished! INFO @ Tue, 16 Jun 2020 09:42:41: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:42:41: #2 alternative fragment length(s) may be 1,10,36,587 bps INFO @ Tue, 16 Jun 2020 09:42:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402698/SRX5402698.05_model.r WARNING @ Tue, 16 Jun 2020 09:42:41: #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 09:42:41: #2 You may need to consider one of the other alternative d(s): 1,10,36,587 WARNING @ Tue, 16 Jun 2020 09:42:41: #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 09:42:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:42:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:42:44: 8000000 INFO @ Tue, 16 Jun 2020 09:42:46: 13000000 INFO @ Tue, 16 Jun 2020 09:42:50: 9000000 INFO @ Tue, 16 Jun 2020 09:42:53: 14000000 INFO @ Tue, 16 Jun 2020 09:42:57: 10000000 INFO @ Tue, 16 Jun 2020 09:42:59: 15000000 INFO @ Tue, 16 Jun 2020 09:43:03: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:43:06: 16000000 INFO @ Tue, 16 Jun 2020 09:43:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:43:10: 12000000 INFO @ Tue, 16 Jun 2020 09:43:12: 17000000 INFO @ Tue, 16 Jun 2020 09:43:14: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:43:14: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:43:14: #1 total tags in treatment: 17225585 INFO @ Tue, 16 Jun 2020 09:43:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:43:14: #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 09:43:14: #1 tags after filtering in treatment: 17225585 INFO @ Tue, 16 Jun 2020 09:43:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:43:14: #1 finished! INFO @ Tue, 16 Jun 2020 09:43:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:43:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:43:15: #2 number of paired peaks: 397 WARNING @ Tue, 16 Jun 2020 09:43:15: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Tue, 16 Jun 2020 09:43:15: start model_add_line... INFO @ Tue, 16 Jun 2020 09:43:15: start X-correlation... INFO @ Tue, 16 Jun 2020 09:43:15: end of X-cor INFO @ Tue, 16 Jun 2020 09:43:15: #2 finished! INFO @ Tue, 16 Jun 2020 09:43:15: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:43:15: #2 alternative fragment length(s) may be 1,10,36,587 bps INFO @ Tue, 16 Jun 2020 09:43:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402698/SRX5402698.10_model.r WARNING @ Tue, 16 Jun 2020 09:43:15: #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 09:43:15: #2 You may need to consider one of the other alternative d(s): 1,10,36,587 WARNING @ Tue, 16 Jun 2020 09:43:15: #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 09:43:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:43:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:43:16: 13000000 INFO @ Tue, 16 Jun 2020 09:43:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402698/SRX5402698.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:43:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402698/SRX5402698.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:43:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402698/SRX5402698.05_summits.bed INFO @ Tue, 16 Jun 2020 09:43:21: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:43:22: 14000000 INFO @ Tue, 16 Jun 2020 09:43:28: 15000000 INFO @ Tue, 16 Jun 2020 09:43:34: 16000000 INFO @ Tue, 16 Jun 2020 09:43:39: 17000000 INFO @ Tue, 16 Jun 2020 09:43:41: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:43:41: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:43:41: #1 total tags in treatment: 17225585 INFO @ Tue, 16 Jun 2020 09:43:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:43:41: #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 09:43:41: #1 tags after filtering in treatment: 17225585 INFO @ Tue, 16 Jun 2020 09:43:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:43:41: #1 finished! INFO @ Tue, 16 Jun 2020 09:43:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:43:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:43:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:43:42: #2 number of paired peaks: 397 WARNING @ Tue, 16 Jun 2020 09:43:42: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Tue, 16 Jun 2020 09:43:42: start model_add_line... INFO @ Tue, 16 Jun 2020 09:43:42: start X-correlation... INFO @ Tue, 16 Jun 2020 09:43:42: end of X-cor INFO @ Tue, 16 Jun 2020 09:43:42: #2 finished! INFO @ Tue, 16 Jun 2020 09:43:42: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:43:42: #2 alternative fragment length(s) may be 1,10,36,587 bps INFO @ Tue, 16 Jun 2020 09:43:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402698/SRX5402698.20_model.r WARNING @ Tue, 16 Jun 2020 09:43:42: #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 09:43:42: #2 You may need to consider one of the other alternative d(s): 1,10,36,587 WARNING @ Tue, 16 Jun 2020 09:43:42: #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 09:43:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:43:42: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:43:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402698/SRX5402698.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:43:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402698/SRX5402698.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:43:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402698/SRX5402698.10_summits.bed INFO @ Tue, 16 Jun 2020 09:43:54: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:44:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:44:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402698/SRX5402698.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:44:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402698/SRX5402698.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:44:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402698/SRX5402698.20_summits.bed INFO @ Tue, 16 Jun 2020 09:44:22: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling