Job ID = 6368743 SRX = SRX5402766 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:25:06 prefetch.2.10.7: 1) Downloading 'SRR8603000'... 2020-06-16T00:25:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:26:50 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:26:51 prefetch.2.10.7: 'SRR8603000' is valid 2020-06-16T00:26:51 prefetch.2.10.7: 1) 'SRR8603000' was downloaded successfully 2020-06-16T00:26:51 prefetch.2.10.7: 'SRR8603000' has 0 unresolved dependencies Read 23657544 spots for SRR8603000/SRR8603000.sra Written 23657544 spots for SRR8603000/SRR8603000.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: 00:05:19 23657544 reads; of these: 23657544 (100.00%) were unpaired; of these: 680484 (2.88%) aligned 0 times 19293348 (81.55%) aligned exactly 1 time 3683712 (15.57%) aligned >1 times 97.12% overall alignment rate Time searching: 00:05:19 Overall time: 00:05:19 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] 5907994 / 22977060 = 0.2571 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 09:37:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402766/SRX5402766.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402766/SRX5402766.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402766/SRX5402766.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402766/SRX5402766.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 09:37:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:37:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:38:02: 1000000 INFO @ Tue, 16 Jun 2020 09:38:07: 2000000 INFO @ Tue, 16 Jun 2020 09:38:12: 3000000 INFO @ Tue, 16 Jun 2020 09:38:17: 4000000 INFO @ Tue, 16 Jun 2020 09:38:22: 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 @ Tue, 16 Jun 2020 09:38:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402766/SRX5402766.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402766/SRX5402766.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402766/SRX5402766.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402766/SRX5402766.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 09:38:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:38:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:38:27: 6000000 INFO @ Tue, 16 Jun 2020 09:38:33: 7000000 INFO @ Tue, 16 Jun 2020 09:38:33: 1000000 INFO @ Tue, 16 Jun 2020 09:38:38: 8000000 INFO @ Tue, 16 Jun 2020 09:38:39: 2000000 INFO @ Tue, 16 Jun 2020 09:38:44: 9000000 INFO @ Tue, 16 Jun 2020 09:38:46: 3000000 INFO @ Tue, 16 Jun 2020 09:38:49: 10000000 INFO @ Tue, 16 Jun 2020 09:38:52: 4000000 INFO @ Tue, 16 Jun 2020 09:38:54: 11000000 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 09:38:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402766/SRX5402766.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402766/SRX5402766.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402766/SRX5402766.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402766/SRX5402766.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 09:38:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:38:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:38:58: 5000000 INFO @ Tue, 16 Jun 2020 09:39:00: 12000000 INFO @ Tue, 16 Jun 2020 09:39:03: 1000000 INFO @ Tue, 16 Jun 2020 09:39:04: 6000000 INFO @ Tue, 16 Jun 2020 09:39:06: 13000000 INFO @ Tue, 16 Jun 2020 09:39:08: 2000000 INFO @ Tue, 16 Jun 2020 09:39:10: 7000000 INFO @ Tue, 16 Jun 2020 09:39:11: 14000000 INFO @ Tue, 16 Jun 2020 09:39:14: 3000000 INFO @ Tue, 16 Jun 2020 09:39:16: 8000000 INFO @ Tue, 16 Jun 2020 09:39:17: 15000000 INFO @ Tue, 16 Jun 2020 09:39:20: 4000000 INFO @ Tue, 16 Jun 2020 09:39:22: 9000000 INFO @ Tue, 16 Jun 2020 09:39:23: 16000000 INFO @ Tue, 16 Jun 2020 09:39:25: 5000000 INFO @ Tue, 16 Jun 2020 09:39:28: 10000000 INFO @ Tue, 16 Jun 2020 09:39:28: 17000000 INFO @ Tue, 16 Jun 2020 09:39:29: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:39:29: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:39:29: #1 total tags in treatment: 17069066 INFO @ Tue, 16 Jun 2020 09:39:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:39:29: #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 09:39:29: #1 tags after filtering in treatment: 17069066 INFO @ Tue, 16 Jun 2020 09:39:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:39:29: #1 finished! INFO @ Tue, 16 Jun 2020 09:39:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:39:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:39:30: #2 number of paired peaks: 229 WARNING @ Tue, 16 Jun 2020 09:39:30: Fewer paired peaks (229) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 229 pairs to build model! INFO @ Tue, 16 Jun 2020 09:39:30: start model_add_line... INFO @ Tue, 16 Jun 2020 09:39:30: start X-correlation... INFO @ Tue, 16 Jun 2020 09:39:30: end of X-cor INFO @ Tue, 16 Jun 2020 09:39:30: #2 finished! INFO @ Tue, 16 Jun 2020 09:39:30: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:39:30: #2 alternative fragment length(s) may be 1,47,520 bps INFO @ Tue, 16 Jun 2020 09:39:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402766/SRX5402766.05_model.r WARNING @ Tue, 16 Jun 2020 09:39:30: #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 09:39:30: #2 You may need to consider one of the other alternative d(s): 1,47,520 WARNING @ Tue, 16 Jun 2020 09:39:30: #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 09:39:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:39:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:39:31: 6000000 INFO @ Tue, 16 Jun 2020 09:39:34: 11000000 INFO @ Tue, 16 Jun 2020 09:39:37: 7000000 INFO @ Tue, 16 Jun 2020 09:39:40: 12000000 INFO @ Tue, 16 Jun 2020 09:39:42: 8000000 INFO @ Tue, 16 Jun 2020 09:39:46: 13000000 INFO @ Tue, 16 Jun 2020 09:39:48: 9000000 INFO @ Tue, 16 Jun 2020 09:39:53: 14000000 INFO @ Tue, 16 Jun 2020 09:39:54: 10000000 INFO @ Tue, 16 Jun 2020 09:39:59: 15000000 INFO @ Tue, 16 Jun 2020 09:39:59: 11000000 INFO @ Tue, 16 Jun 2020 09:39:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:40:05: 12000000 INFO @ Tue, 16 Jun 2020 09:40:05: 16000000 INFO @ Tue, 16 Jun 2020 09:40:12: 13000000 INFO @ Tue, 16 Jun 2020 09:40:12: 17000000 INFO @ Tue, 16 Jun 2020 09:40:12: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:40:12: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:40:12: #1 total tags in treatment: 17069066 INFO @ Tue, 16 Jun 2020 09:40:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:40:12: #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 09:40:12: #1 tags after filtering in treatment: 17069066 INFO @ Tue, 16 Jun 2020 09:40:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:40:12: #1 finished! INFO @ Tue, 16 Jun 2020 09:40:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:40:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:40:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402766/SRX5402766.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:40:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402766/SRX5402766.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:40:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402766/SRX5402766.05_summits.bed INFO @ Tue, 16 Jun 2020 09:40:13: Done! INFO @ Tue, 16 Jun 2020 09:40:14: #2 number of paired peaks: 229 WARNING @ Tue, 16 Jun 2020 09:40:14: Fewer paired peaks (229) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 229 pairs to build model! INFO @ Tue, 16 Jun 2020 09:40:14: start model_add_line... pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:40:14: start X-correlation... INFO @ Tue, 16 Jun 2020 09:40:14: end of X-cor INFO @ Tue, 16 Jun 2020 09:40:14: #2 finished! INFO @ Tue, 16 Jun 2020 09:40:14: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:40:14: #2 alternative fragment length(s) may be 1,47,520 bps INFO @ Tue, 16 Jun 2020 09:40:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402766/SRX5402766.10_model.r WARNING @ Tue, 16 Jun 2020 09:40:14: #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 09:40:14: #2 You may need to consider one of the other alternative d(s): 1,47,520 WARNING @ Tue, 16 Jun 2020 09:40:14: #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 09:40:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:40:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:40:17: 14000000 INFO @ Tue, 16 Jun 2020 09:40:23: 15000000 INFO @ Tue, 16 Jun 2020 09:40:28: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:40:33: 17000000 INFO @ Tue, 16 Jun 2020 09:40:34: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:40:34: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:40:34: #1 total tags in treatment: 17069066 INFO @ Tue, 16 Jun 2020 09:40:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:40:34: #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 09:40:34: #1 tags after filtering in treatment: 17069066 INFO @ Tue, 16 Jun 2020 09:40:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:40:34: #1 finished! INFO @ Tue, 16 Jun 2020 09:40:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:40:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:40:35: #2 number of paired peaks: 229 WARNING @ Tue, 16 Jun 2020 09:40:35: Fewer paired peaks (229) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 229 pairs to build model! INFO @ Tue, 16 Jun 2020 09:40:35: start model_add_line... INFO @ Tue, 16 Jun 2020 09:40:35: start X-correlation... INFO @ Tue, 16 Jun 2020 09:40:35: end of X-cor INFO @ Tue, 16 Jun 2020 09:40:35: #2 finished! INFO @ Tue, 16 Jun 2020 09:40:35: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:40:35: #2 alternative fragment length(s) may be 1,47,520 bps INFO @ Tue, 16 Jun 2020 09:40:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402766/SRX5402766.20_model.r WARNING @ Tue, 16 Jun 2020 09:40:35: #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 09:40:35: #2 You may need to consider one of the other alternative d(s): 1,47,520 WARNING @ Tue, 16 Jun 2020 09:40:35: #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 09:40:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:40:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:40:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:40:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402766/SRX5402766.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:40:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402766/SRX5402766.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:40:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402766/SRX5402766.10_summits.bed INFO @ Tue, 16 Jun 2020 09:40:55: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:41:03: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:41:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402766/SRX5402766.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:41:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402766/SRX5402766.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:41:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402766/SRX5402766.20_summits.bed INFO @ Tue, 16 Jun 2020 09:41:17: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling