Job ID = 6368786 SRX = SRX5702593 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:24:36 prefetch.2.10.7: 1) Downloading 'SRR8921267'... 2020-06-16T00:24:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:25:57 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:25:58 prefetch.2.10.7: 'SRR8921267' is valid 2020-06-16T00:25:58 prefetch.2.10.7: 1) 'SRR8921267' was downloaded successfully 2020-06-16T00:25:58 prefetch.2.10.7: 'SRR8921267' has 0 unresolved dependencies Read 25678942 spots for SRR8921267/SRR8921267.sra Written 25678942 spots for SRR8921267/SRR8921267.sra 2020-06-16T00:27:29 prefetch.2.10.7: 1) Downloading 'SRR8921268'... 2020-06-16T00:27:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:28:56 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:28:56 prefetch.2.10.7: 'SRR8921268' is valid 2020-06-16T00:28:56 prefetch.2.10.7: 1) 'SRR8921268' was downloaded successfully 2020-06-16T00:28:56 prefetch.2.10.7: 'SRR8921268' has 0 unresolved dependencies Read 22318508 spots for SRR8921268/SRR8921268.sra Written 22318508 spots for SRR8921268/SRR8921268.sra 2020-06-16T00:30:17 prefetch.2.10.7: 1) Downloading 'SRR8921269'... 2020-06-16T00:30:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:37:22 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:37:22 prefetch.2.10.7: 1) 'SRR8921269' was downloaded successfully 2020-06-16T00:37:22 prefetch.2.10.7: 'SRR8921269' has 0 unresolved dependencies Read 54753982 spots for SRR8921269/SRR8921269.sra Written 54753982 spots for SRR8921269/SRR8921269.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: 00:21:12 102751432 reads; of these: 102751432 (100.00%) were unpaired; of these: 43078817 (41.93%) aligned 0 times 46193838 (44.96%) aligned exactly 1 time 13478777 (13.12%) aligned >1 times 58.07% overall alignment rate Time searching: 00:21:12 Overall time: 00:21:12 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 28 files... [bam_rmdupse_core] 35879144 / 59672615 = 0.6013 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 10:13:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5702593/SRX5702593.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5702593/SRX5702593.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5702593/SRX5702593.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5702593/SRX5702593.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 10:13:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:13:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:13:16: 1000000 INFO @ Tue, 16 Jun 2020 10:13:23: 2000000 INFO @ Tue, 16 Jun 2020 10:13:31: 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 10:13:38: 4000000 INFO @ Tue, 16 Jun 2020 10:13:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5702593/SRX5702593.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5702593/SRX5702593.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5702593/SRX5702593.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5702593/SRX5702593.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 10:13:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:13:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:13:45: 5000000 INFO @ Tue, 16 Jun 2020 10:13:46: 1000000 INFO @ Tue, 16 Jun 2020 10:13:53: 6000000 INFO @ Tue, 16 Jun 2020 10:13:53: 2000000 INFO @ Tue, 16 Jun 2020 10:14:00: 3000000 INFO @ Tue, 16 Jun 2020 10:14:01: 7000000 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 10:14:08: 4000000 INFO @ Tue, 16 Jun 2020 10:14:09: 8000000 INFO @ Tue, 16 Jun 2020 10:14:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5702593/SRX5702593.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5702593/SRX5702593.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5702593/SRX5702593.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5702593/SRX5702593.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 10:14:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:14:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:14:15: 5000000 INFO @ Tue, 16 Jun 2020 10:14:16: 1000000 INFO @ Tue, 16 Jun 2020 10:14:16: 9000000 INFO @ Tue, 16 Jun 2020 10:14:22: 6000000 INFO @ Tue, 16 Jun 2020 10:14:23: 2000000 INFO @ Tue, 16 Jun 2020 10:14:24: 10000000 INFO @ Tue, 16 Jun 2020 10:14:29: 7000000 INFO @ Tue, 16 Jun 2020 10:14:31: 3000000 INFO @ Tue, 16 Jun 2020 10:14:32: 11000000 INFO @ Tue, 16 Jun 2020 10:14:37: 8000000 INFO @ Tue, 16 Jun 2020 10:14:38: 4000000 INFO @ Tue, 16 Jun 2020 10:14:40: 12000000 INFO @ Tue, 16 Jun 2020 10:14:44: 9000000 INFO @ Tue, 16 Jun 2020 10:14:45: 5000000 INFO @ Tue, 16 Jun 2020 10:14:48: 13000000 INFO @ Tue, 16 Jun 2020 10:14:51: 10000000 INFO @ Tue, 16 Jun 2020 10:14:53: 6000000 INFO @ Tue, 16 Jun 2020 10:14:55: 14000000 INFO @ Tue, 16 Jun 2020 10:14:59: 11000000 INFO @ Tue, 16 Jun 2020 10:15:00: 7000000 INFO @ Tue, 16 Jun 2020 10:15:03: 15000000 INFO @ Tue, 16 Jun 2020 10:15:06: 12000000 INFO @ Tue, 16 Jun 2020 10:15:07: 8000000 INFO @ Tue, 16 Jun 2020 10:15:11: 16000000 INFO @ Tue, 16 Jun 2020 10:15:13: 13000000 INFO @ Tue, 16 Jun 2020 10:15:14: 9000000 INFO @ Tue, 16 Jun 2020 10:15:19: 17000000 INFO @ Tue, 16 Jun 2020 10:15:20: 14000000 INFO @ Tue, 16 Jun 2020 10:15:22: 10000000 INFO @ Tue, 16 Jun 2020 10:15:27: 18000000 INFO @ Tue, 16 Jun 2020 10:15:27: 15000000 INFO @ Tue, 16 Jun 2020 10:15:29: 11000000 INFO @ Tue, 16 Jun 2020 10:15:34: 19000000 INFO @ Tue, 16 Jun 2020 10:15:35: 16000000 INFO @ Tue, 16 Jun 2020 10:15:36: 12000000 INFO @ Tue, 16 Jun 2020 10:15:42: 17000000 INFO @ Tue, 16 Jun 2020 10:15:42: 20000000 INFO @ Tue, 16 Jun 2020 10:15:43: 13000000 INFO @ Tue, 16 Jun 2020 10:15:49: 18000000 INFO @ Tue, 16 Jun 2020 10:15:50: 21000000 INFO @ Tue, 16 Jun 2020 10:15:51: 14000000 INFO @ Tue, 16 Jun 2020 10:15:56: 19000000 INFO @ Tue, 16 Jun 2020 10:15:57: 22000000 INFO @ Tue, 16 Jun 2020 10:15:58: 15000000 INFO @ Tue, 16 Jun 2020 10:16:03: 20000000 INFO @ Tue, 16 Jun 2020 10:16:05: 16000000 INFO @ Tue, 16 Jun 2020 10:16:05: 23000000 INFO @ Tue, 16 Jun 2020 10:16:11: 21000000 INFO @ Tue, 16 Jun 2020 10:16:11: #1 tag size is determined as 55 bps INFO @ Tue, 16 Jun 2020 10:16:11: #1 tag size = 55 INFO @ Tue, 16 Jun 2020 10:16:11: #1 total tags in treatment: 23793471 INFO @ Tue, 16 Jun 2020 10:16:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:16:11: #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 10:16:12: #1 tags after filtering in treatment: 23793471 INFO @ Tue, 16 Jun 2020 10:16:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:16:12: #1 finished! INFO @ Tue, 16 Jun 2020 10:16:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:16:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:16:12: 17000000 INFO @ Tue, 16 Jun 2020 10:16:13: #2 number of paired peaks: 247 WARNING @ Tue, 16 Jun 2020 10:16:13: Fewer paired peaks (247) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 247 pairs to build model! INFO @ Tue, 16 Jun 2020 10:16:13: start model_add_line... INFO @ Tue, 16 Jun 2020 10:16:13: start X-correlation... INFO @ Tue, 16 Jun 2020 10:16:14: end of X-cor INFO @ Tue, 16 Jun 2020 10:16:14: #2 finished! INFO @ Tue, 16 Jun 2020 10:16:14: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 10:16:14: #2 alternative fragment length(s) may be 1,29,555,592 bps INFO @ Tue, 16 Jun 2020 10:16:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5702593/SRX5702593.05_model.r WARNING @ Tue, 16 Jun 2020 10:16:14: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:16:14: #2 You may need to consider one of the other alternative d(s): 1,29,555,592 WARNING @ Tue, 16 Jun 2020 10:16:14: #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 10:16:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:16:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:16:18: 22000000 INFO @ Tue, 16 Jun 2020 10:16:19: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:16:24: 23000000 INFO @ Tue, 16 Jun 2020 10:16:27: 19000000 INFO @ Tue, 16 Jun 2020 10:16:30: #1 tag size is determined as 55 bps INFO @ Tue, 16 Jun 2020 10:16:30: #1 tag size = 55 INFO @ Tue, 16 Jun 2020 10:16:30: #1 total tags in treatment: 23793471 INFO @ Tue, 16 Jun 2020 10:16:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:16:30: #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 10:16:30: #1 tags after filtering in treatment: 23793471 INFO @ Tue, 16 Jun 2020 10:16:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:16:30: #1 finished! INFO @ Tue, 16 Jun 2020 10:16:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:16:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:16:32: #2 number of paired peaks: 247 WARNING @ Tue, 16 Jun 2020 10:16:32: Fewer paired peaks (247) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 247 pairs to build model! INFO @ Tue, 16 Jun 2020 10:16:32: start model_add_line... INFO @ Tue, 16 Jun 2020 10:16:32: start X-correlation... INFO @ Tue, 16 Jun 2020 10:16:32: end of X-cor INFO @ Tue, 16 Jun 2020 10:16:32: #2 finished! INFO @ Tue, 16 Jun 2020 10:16:32: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 10:16:32: #2 alternative fragment length(s) may be 1,29,555,592 bps INFO @ Tue, 16 Jun 2020 10:16:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5702593/SRX5702593.10_model.r WARNING @ Tue, 16 Jun 2020 10:16:32: #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 10:16:32: #2 You may need to consider one of the other alternative d(s): 1,29,555,592 WARNING @ Tue, 16 Jun 2020 10:16:32: #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 10:16:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:16:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:16:33: 20000000 INFO @ Tue, 16 Jun 2020 10:16:40: 21000000 INFO @ Tue, 16 Jun 2020 10:16:46: 22000000 INFO @ Tue, 16 Jun 2020 10:16:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:16:52: 23000000 INFO @ Tue, 16 Jun 2020 10:16:57: #1 tag size is determined as 55 bps INFO @ Tue, 16 Jun 2020 10:16:57: #1 tag size = 55 INFO @ Tue, 16 Jun 2020 10:16:57: #1 total tags in treatment: 23793471 INFO @ Tue, 16 Jun 2020 10:16:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:16:57: #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 10:16:58: #1 tags after filtering in treatment: 23793471 INFO @ Tue, 16 Jun 2020 10:16:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:16:58: #1 finished! INFO @ Tue, 16 Jun 2020 10:16:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:16:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:16:59: #2 number of paired peaks: 247 WARNING @ Tue, 16 Jun 2020 10:16:59: Fewer paired peaks (247) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 247 pairs to build model! INFO @ Tue, 16 Jun 2020 10:16:59: start model_add_line... INFO @ Tue, 16 Jun 2020 10:16:59: start X-correlation... INFO @ Tue, 16 Jun 2020 10:16:59: end of X-cor INFO @ Tue, 16 Jun 2020 10:16:59: #2 finished! INFO @ Tue, 16 Jun 2020 10:16:59: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 10:16:59: #2 alternative fragment length(s) may be 1,29,555,592 bps INFO @ Tue, 16 Jun 2020 10:16:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5702593/SRX5702593.20_model.r WARNING @ Tue, 16 Jun 2020 10:16:59: #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 10:16:59: #2 You may need to consider one of the other alternative d(s): 1,29,555,592 WARNING @ Tue, 16 Jun 2020 10:16:59: #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 10:16:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:16:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:17:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5702593/SRX5702593.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:17:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5702593/SRX5702593.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:17:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5702593/SRX5702593.05_summits.bed INFO @ Tue, 16 Jun 2020 10:17:08: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:17:09: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:17:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5702593/SRX5702593.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:17:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5702593/SRX5702593.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:17:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5702593/SRX5702593.10_summits.bed INFO @ Tue, 16 Jun 2020 10:17:28: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:17:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:17:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5702593/SRX5702593.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:17:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5702593/SRX5702593.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:17:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5702593/SRX5702593.20_summits.bed INFO @ Tue, 16 Jun 2020 10:17:55: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling