Job ID = 6368679 SRX = SRX5402706 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:20:24 prefetch.2.10.7: 1) Downloading 'SRR8602940'... 2020-06-16T00:20:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:23:08 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:23:08 prefetch.2.10.7: 1) 'SRR8602940' was downloaded successfully Read 24297646 spots for SRR8602940/SRR8602940.sra Written 24297646 spots for SRR8602940/SRR8602940.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: 00:05:06 24297646 reads; of these: 24297646 (100.00%) were unpaired; of these: 1569181 (6.46%) aligned 0 times 19711028 (81.12%) aligned exactly 1 time 3017437 (12.42%) aligned >1 times 93.54% overall alignment rate Time searching: 00:05:06 Overall time: 00:05:06 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] 3368857 / 22728465 = 0.1482 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 09:36:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402706/SRX5402706.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402706/SRX5402706.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402706/SRX5402706.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402706/SRX5402706.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 09:36:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:36:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:36:45: 1000000 INFO @ Tue, 16 Jun 2020 09:36:51: 2000000 INFO @ Tue, 16 Jun 2020 09:36:56: 3000000 INFO @ Tue, 16 Jun 2020 09:37:02: 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 09:37:08: 5000000 INFO @ Tue, 16 Jun 2020 09:37:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402706/SRX5402706.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402706/SRX5402706.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402706/SRX5402706.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402706/SRX5402706.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 09:37:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:37:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:37:14: 6000000 INFO @ Tue, 16 Jun 2020 09:37:15: 1000000 INFO @ Tue, 16 Jun 2020 09:37:20: 7000000 INFO @ Tue, 16 Jun 2020 09:37:21: 2000000 INFO @ Tue, 16 Jun 2020 09:37:26: 8000000 INFO @ Tue, 16 Jun 2020 09:37:27: 3000000 INFO @ Tue, 16 Jun 2020 09:37:32: 9000000 INFO @ Tue, 16 Jun 2020 09:37:33: 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 09:37:39: 10000000 INFO @ Tue, 16 Jun 2020 09:37:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402706/SRX5402706.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402706/SRX5402706.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402706/SRX5402706.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402706/SRX5402706.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 09:37:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:37:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:37:40: 5000000 INFO @ Tue, 16 Jun 2020 09:37:45: 11000000 INFO @ Tue, 16 Jun 2020 09:37:45: 1000000 INFO @ Tue, 16 Jun 2020 09:37:46: 6000000 INFO @ Tue, 16 Jun 2020 09:37:51: 2000000 INFO @ Tue, 16 Jun 2020 09:37:51: 12000000 INFO @ Tue, 16 Jun 2020 09:37:52: 7000000 INFO @ Tue, 16 Jun 2020 09:37:57: 3000000 INFO @ Tue, 16 Jun 2020 09:37:58: 13000000 INFO @ Tue, 16 Jun 2020 09:37:59: 8000000 INFO @ Tue, 16 Jun 2020 09:38:03: 4000000 INFO @ Tue, 16 Jun 2020 09:38:04: 14000000 INFO @ Tue, 16 Jun 2020 09:38:05: 9000000 INFO @ Tue, 16 Jun 2020 09:38:09: 5000000 INFO @ Tue, 16 Jun 2020 09:38:10: 15000000 INFO @ Tue, 16 Jun 2020 09:38:11: 10000000 INFO @ Tue, 16 Jun 2020 09:38:15: 6000000 INFO @ Tue, 16 Jun 2020 09:38:17: 16000000 INFO @ Tue, 16 Jun 2020 09:38:18: 11000000 INFO @ Tue, 16 Jun 2020 09:38:21: 7000000 INFO @ Tue, 16 Jun 2020 09:38:23: 17000000 INFO @ Tue, 16 Jun 2020 09:38:24: 12000000 INFO @ Tue, 16 Jun 2020 09:38:27: 8000000 INFO @ Tue, 16 Jun 2020 09:38:29: 18000000 INFO @ Tue, 16 Jun 2020 09:38:30: 13000000 INFO @ Tue, 16 Jun 2020 09:38:33: 9000000 INFO @ Tue, 16 Jun 2020 09:38:36: 19000000 INFO @ Tue, 16 Jun 2020 09:38:37: 14000000 INFO @ Tue, 16 Jun 2020 09:38:38: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:38:38: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:38:38: #1 total tags in treatment: 19359608 INFO @ Tue, 16 Jun 2020 09:38:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:38:38: #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 09:38:38: #1 tags after filtering in treatment: 19359608 INFO @ Tue, 16 Jun 2020 09:38:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:38:38: #1 finished! INFO @ Tue, 16 Jun 2020 09:38:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:38:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:38:39: 10000000 INFO @ Tue, 16 Jun 2020 09:38:40: #2 number of paired peaks: 131 WARNING @ Tue, 16 Jun 2020 09:38:40: Fewer paired peaks (131) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 131 pairs to build model! INFO @ Tue, 16 Jun 2020 09:38:40: start model_add_line... INFO @ Tue, 16 Jun 2020 09:38:40: start X-correlation... INFO @ Tue, 16 Jun 2020 09:38:40: end of X-cor INFO @ Tue, 16 Jun 2020 09:38:40: #2 finished! INFO @ Tue, 16 Jun 2020 09:38:40: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:38:40: #2 alternative fragment length(s) may be 1,32,45,524,562 bps INFO @ Tue, 16 Jun 2020 09:38:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402706/SRX5402706.05_model.r WARNING @ Tue, 16 Jun 2020 09:38:40: #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 09:38:40: #2 You may need to consider one of the other alternative d(s): 1,32,45,524,562 WARNING @ Tue, 16 Jun 2020 09:38:40: #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 09:38:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:38:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:38:43: 15000000 INFO @ Tue, 16 Jun 2020 09:38:45: 11000000 INFO @ Tue, 16 Jun 2020 09:38:49: 16000000 INFO @ Tue, 16 Jun 2020 09:38:51: 12000000 INFO @ Tue, 16 Jun 2020 09:38:55: 17000000 INFO @ Tue, 16 Jun 2020 09:38:57: 13000000 INFO @ Tue, 16 Jun 2020 09:39:01: 18000000 INFO @ Tue, 16 Jun 2020 09:39:02: 14000000 INFO @ Tue, 16 Jun 2020 09:39:07: 19000000 INFO @ Tue, 16 Jun 2020 09:39:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:39:08: 15000000 INFO @ Tue, 16 Jun 2020 09:39:09: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:39:09: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:39:09: #1 total tags in treatment: 19359608 INFO @ Tue, 16 Jun 2020 09:39:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:39:09: #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 09:39:10: #1 tags after filtering in treatment: 19359608 INFO @ Tue, 16 Jun 2020 09:39:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:39:10: #1 finished! INFO @ Tue, 16 Jun 2020 09:39:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:39:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:39:11: #2 number of paired peaks: 131 WARNING @ Tue, 16 Jun 2020 09:39:11: Fewer paired peaks (131) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 131 pairs to build model! INFO @ Tue, 16 Jun 2020 09:39:11: start model_add_line... INFO @ Tue, 16 Jun 2020 09:39:11: start X-correlation... INFO @ Tue, 16 Jun 2020 09:39:11: end of X-cor INFO @ Tue, 16 Jun 2020 09:39:11: #2 finished! INFO @ Tue, 16 Jun 2020 09:39:11: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:39:11: #2 alternative fragment length(s) may be 1,32,45,524,562 bps INFO @ Tue, 16 Jun 2020 09:39:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402706/SRX5402706.10_model.r WARNING @ Tue, 16 Jun 2020 09:39:11: #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 09:39:11: #2 You may need to consider one of the other alternative d(s): 1,32,45,524,562 WARNING @ Tue, 16 Jun 2020 09:39:11: #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 09:39:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:39:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:39:14: 16000000 INFO @ Tue, 16 Jun 2020 09:39:20: 17000000 INFO @ Tue, 16 Jun 2020 09:39:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402706/SRX5402706.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:39:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402706/SRX5402706.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:39:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402706/SRX5402706.05_summits.bed INFO @ Tue, 16 Jun 2020 09:39:21: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:39:25: 18000000 INFO @ Tue, 16 Jun 2020 09:39:31: 19000000 INFO @ Tue, 16 Jun 2020 09:39:33: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:39:33: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:39:33: #1 total tags in treatment: 19359608 INFO @ Tue, 16 Jun 2020 09:39:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:39:33: #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 09:39:33: #1 tags after filtering in treatment: 19359608 INFO @ Tue, 16 Jun 2020 09:39:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:39:33: #1 finished! INFO @ Tue, 16 Jun 2020 09:39:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:39:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:39:35: #2 number of paired peaks: 131 WARNING @ Tue, 16 Jun 2020 09:39:35: Fewer paired peaks (131) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 131 pairs to build model! INFO @ Tue, 16 Jun 2020 09:39:35: start model_add_line... INFO @ Tue, 16 Jun 2020 09:39:35: start X-correlation... INFO @ Tue, 16 Jun 2020 09:39:35: end of X-cor INFO @ Tue, 16 Jun 2020 09:39:35: #2 finished! INFO @ Tue, 16 Jun 2020 09:39:35: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:39:35: #2 alternative fragment length(s) may be 1,32,45,524,562 bps INFO @ Tue, 16 Jun 2020 09:39:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402706/SRX5402706.20_model.r WARNING @ Tue, 16 Jun 2020 09:39:35: #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 09:39:35: #2 You may need to consider one of the other alternative d(s): 1,32,45,524,562 WARNING @ Tue, 16 Jun 2020 09:39:35: #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 09:39:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:39:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:39:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:39:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402706/SRX5402706.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:39:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402706/SRX5402706.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:39:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402706/SRX5402706.10_summits.bed INFO @ Tue, 16 Jun 2020 09:39:52: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:40:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:40:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402706/SRX5402706.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:40:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402706/SRX5402706.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:40:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402706/SRX5402706.20_summits.bed INFO @ Tue, 16 Jun 2020 09:40:15: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。