Job ID = 6368784 SRX = SRX5702591 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:30:45 prefetch.2.10.7: 1) Downloading 'SRR8921262'... 2020-06-16T00:30:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:32:15 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:32:16 prefetch.2.10.7: 'SRR8921262' is valid 2020-06-16T00:32:16 prefetch.2.10.7: 1) 'SRR8921262' was downloaded successfully 2020-06-16T00:32:16 prefetch.2.10.7: 'SRR8921262' has 0 unresolved dependencies Read 26012368 spots for SRR8921262/SRR8921262.sra Written 26012368 spots for SRR8921262/SRR8921262.sra 2020-06-16T00:33:49 prefetch.2.10.7: 1) Downloading 'SRR8921263'... 2020-06-16T00:33:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:35:10 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:35:11 prefetch.2.10.7: 'SRR8921263' is valid 2020-06-16T00:35:11 prefetch.2.10.7: 1) 'SRR8921263' was downloaded successfully 2020-06-16T00:35:11 prefetch.2.10.7: 'SRR8921263' has 0 unresolved dependencies Read 20055199 spots for SRR8921263/SRR8921263.sra Written 20055199 spots for SRR8921263/SRR8921263.sra 2020-06-16T00:36:24 prefetch.2.10.7: 1) Downloading 'SRR8921264'... 2020-06-16T00:36:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:39:52 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:39:52 prefetch.2.10.7: 1) 'SRR8921264' was downloaded successfully 2020-06-16T00:39:52 prefetch.2.10.7: 'SRR8921264' has 0 unresolved dependencies Read 40961267 spots for SRR8921264/SRR8921264.sra Written 40961267 spots for SRR8921264/SRR8921264.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: 00:19:20 87028834 reads; of these: 87028834 (100.00%) were unpaired; of these: 35762495 (41.09%) aligned 0 times 38372646 (44.09%) aligned exactly 1 time 12893693 (14.82%) aligned >1 times 58.91% overall alignment rate Time searching: 00:19:20 Overall time: 00:19:20 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 24 files... [bam_rmdupse_core] 23642956 / 51266339 = 0.4612 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 10:12:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5702591/SRX5702591.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5702591/SRX5702591.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5702591/SRX5702591.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5702591/SRX5702591.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 10:12:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:12:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:12:09: 1000000 INFO @ Tue, 16 Jun 2020 10:12:15: 2000000 INFO @ Tue, 16 Jun 2020 10:12:21: 3000000 INFO @ Tue, 16 Jun 2020 10:12:27: 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 10:12:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5702591/SRX5702591.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5702591/SRX5702591.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5702591/SRX5702591.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5702591/SRX5702591.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 10:12:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:12:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:12:33: 5000000 INFO @ Tue, 16 Jun 2020 10:12:39: 1000000 INFO @ Tue, 16 Jun 2020 10:12:40: 6000000 INFO @ Tue, 16 Jun 2020 10:12:46: 2000000 INFO @ Tue, 16 Jun 2020 10:12:46: 7000000 INFO @ Tue, 16 Jun 2020 10:12:52: 3000000 INFO @ Tue, 16 Jun 2020 10:12:53: 8000000 INFO @ Tue, 16 Jun 2020 10:12:59: 4000000 INFO @ Tue, 16 Jun 2020 10:12:59: 9000000 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 10:13:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5702591/SRX5702591.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5702591/SRX5702591.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5702591/SRX5702591.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5702591/SRX5702591.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 10:13:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:13:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:13:06: 5000000 INFO @ Tue, 16 Jun 2020 10:13:06: 10000000 INFO @ Tue, 16 Jun 2020 10:13:11: 1000000 INFO @ Tue, 16 Jun 2020 10:13:13: 6000000 INFO @ Tue, 16 Jun 2020 10:13:14: 11000000 INFO @ Tue, 16 Jun 2020 10:13:19: 2000000 INFO @ Tue, 16 Jun 2020 10:13:21: 7000000 INFO @ Tue, 16 Jun 2020 10:13:21: 12000000 INFO @ Tue, 16 Jun 2020 10:13:27: 3000000 INFO @ Tue, 16 Jun 2020 10:13:29: 8000000 INFO @ Tue, 16 Jun 2020 10:13:29: 13000000 INFO @ Tue, 16 Jun 2020 10:13:36: 4000000 INFO @ Tue, 16 Jun 2020 10:13:36: 9000000 INFO @ Tue, 16 Jun 2020 10:13:37: 14000000 INFO @ Tue, 16 Jun 2020 10:13:44: 10000000 INFO @ Tue, 16 Jun 2020 10:13:44: 5000000 INFO @ Tue, 16 Jun 2020 10:13:44: 15000000 INFO @ Tue, 16 Jun 2020 10:13:51: 11000000 INFO @ Tue, 16 Jun 2020 10:13:51: 16000000 INFO @ Tue, 16 Jun 2020 10:13:52: 6000000 INFO @ Tue, 16 Jun 2020 10:13:58: 12000000 INFO @ Tue, 16 Jun 2020 10:13:59: 17000000 INFO @ Tue, 16 Jun 2020 10:14:00: 7000000 INFO @ Tue, 16 Jun 2020 10:14:06: 13000000 INFO @ Tue, 16 Jun 2020 10:14:06: 18000000 INFO @ Tue, 16 Jun 2020 10:14:08: 8000000 INFO @ Tue, 16 Jun 2020 10:14:13: 14000000 INFO @ Tue, 16 Jun 2020 10:14:14: 19000000 INFO @ Tue, 16 Jun 2020 10:14:16: 9000000 INFO @ Tue, 16 Jun 2020 10:14:21: 15000000 INFO @ Tue, 16 Jun 2020 10:14:21: 20000000 INFO @ Tue, 16 Jun 2020 10:14:24: 10000000 INFO @ Tue, 16 Jun 2020 10:14:28: 16000000 INFO @ Tue, 16 Jun 2020 10:14:29: 21000000 INFO @ Tue, 16 Jun 2020 10:14:32: 11000000 INFO @ Tue, 16 Jun 2020 10:14:36: 17000000 INFO @ Tue, 16 Jun 2020 10:14:36: 22000000 INFO @ Tue, 16 Jun 2020 10:14:41: 12000000 INFO @ Tue, 16 Jun 2020 10:14:43: 18000000 INFO @ Tue, 16 Jun 2020 10:14:44: 23000000 INFO @ Tue, 16 Jun 2020 10:14:49: 13000000 INFO @ Tue, 16 Jun 2020 10:14:51: 19000000 INFO @ Tue, 16 Jun 2020 10:14:51: 24000000 INFO @ Tue, 16 Jun 2020 10:14:57: 14000000 INFO @ Tue, 16 Jun 2020 10:14:58: 20000000 INFO @ Tue, 16 Jun 2020 10:14:59: 25000000 INFO @ Tue, 16 Jun 2020 10:15:05: 15000000 INFO @ Tue, 16 Jun 2020 10:15:06: 21000000 INFO @ Tue, 16 Jun 2020 10:15:06: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:15:13: 16000000 INFO @ Tue, 16 Jun 2020 10:15:14: 22000000 INFO @ Tue, 16 Jun 2020 10:15:14: 27000000 INFO @ Tue, 16 Jun 2020 10:15:19: #1 tag size is determined as 55 bps INFO @ Tue, 16 Jun 2020 10:15:19: #1 tag size = 55 INFO @ Tue, 16 Jun 2020 10:15:19: #1 total tags in treatment: 27623383 INFO @ Tue, 16 Jun 2020 10:15:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:15:19: #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 10:15:19: #1 tags after filtering in treatment: 27623383 INFO @ Tue, 16 Jun 2020 10:15:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:15:19: #1 finished! INFO @ Tue, 16 Jun 2020 10:15:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:15:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:15:21: 23000000 INFO @ Tue, 16 Jun 2020 10:15:21: #2 number of paired peaks: 217 WARNING @ Tue, 16 Jun 2020 10:15:21: Fewer paired peaks (217) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 217 pairs to build model! INFO @ Tue, 16 Jun 2020 10:15:21: start model_add_line... INFO @ Tue, 16 Jun 2020 10:15:21: start X-correlation... INFO @ Tue, 16 Jun 2020 10:15:21: end of X-cor INFO @ Tue, 16 Jun 2020 10:15:21: #2 finished! INFO @ Tue, 16 Jun 2020 10:15:21: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 10:15:21: #2 alternative fragment length(s) may be 1,20,48,537,554 bps INFO @ Tue, 16 Jun 2020 10:15:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5702591/SRX5702591.05_model.r WARNING @ Tue, 16 Jun 2020 10:15:21: #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 10:15:21: #2 You may need to consider one of the other alternative d(s): 1,20,48,537,554 WARNING @ Tue, 16 Jun 2020 10:15:21: #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 10:15:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:15:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:15:21: 17000000 INFO @ Tue, 16 Jun 2020 10:15:28: 24000000 INFO @ Tue, 16 Jun 2020 10:15:29: 18000000 INFO @ Tue, 16 Jun 2020 10:15:35: 25000000 INFO @ Tue, 16 Jun 2020 10:15:37: 19000000 INFO @ Tue, 16 Jun 2020 10:15:43: 26000000 INFO @ Tue, 16 Jun 2020 10:15:45: 20000000 INFO @ Tue, 16 Jun 2020 10:15:50: 27000000 INFO @ Tue, 16 Jun 2020 10:15:53: 21000000 INFO @ Tue, 16 Jun 2020 10:15:55: #1 tag size is determined as 55 bps INFO @ Tue, 16 Jun 2020 10:15:55: #1 tag size = 55 INFO @ Tue, 16 Jun 2020 10:15:55: #1 total tags in treatment: 27623383 INFO @ Tue, 16 Jun 2020 10:15:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:15:55: #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 10:15:55: #1 tags after filtering in treatment: 27623383 INFO @ Tue, 16 Jun 2020 10:15:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:15:55: #1 finished! INFO @ Tue, 16 Jun 2020 10:15:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:15:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:15:57: #2 number of paired peaks: 217 WARNING @ Tue, 16 Jun 2020 10:15:57: Fewer paired peaks (217) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 217 pairs to build model! INFO @ Tue, 16 Jun 2020 10:15:57: start model_add_line... INFO @ Tue, 16 Jun 2020 10:15:57: start X-correlation... INFO @ Tue, 16 Jun 2020 10:15:57: end of X-cor INFO @ Tue, 16 Jun 2020 10:15:57: #2 finished! INFO @ Tue, 16 Jun 2020 10:15:57: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 10:15:57: #2 alternative fragment length(s) may be 1,20,48,537,554 bps INFO @ Tue, 16 Jun 2020 10:15:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5702591/SRX5702591.10_model.r WARNING @ Tue, 16 Jun 2020 10:15:57: #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 10:15:57: #2 You may need to consider one of the other alternative d(s): 1,20,48,537,554 WARNING @ Tue, 16 Jun 2020 10:15:57: #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 10:15:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:15:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:16:00: 22000000 INFO @ Tue, 16 Jun 2020 10:16:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:16:07: 23000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:16:15: 24000000 INFO @ Tue, 16 Jun 2020 10:16:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5702591/SRX5702591.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:16:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5702591/SRX5702591.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:16:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5702591/SRX5702591.05_summits.bed INFO @ Tue, 16 Jun 2020 10:16:19: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:16:22: 25000000 INFO @ Tue, 16 Jun 2020 10:16:29: 26000000 INFO @ Tue, 16 Jun 2020 10:16:36: 27000000 INFO @ Tue, 16 Jun 2020 10:16:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:16:41: #1 tag size is determined as 55 bps INFO @ Tue, 16 Jun 2020 10:16:41: #1 tag size = 55 INFO @ Tue, 16 Jun 2020 10:16:41: #1 total tags in treatment: 27623383 INFO @ Tue, 16 Jun 2020 10:16:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:16:41: #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 10:16:41: #1 tags after filtering in treatment: 27623383 INFO @ Tue, 16 Jun 2020 10:16:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:16:41: #1 finished! INFO @ Tue, 16 Jun 2020 10:16:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:16:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:16:43: #2 number of paired peaks: 217 WARNING @ Tue, 16 Jun 2020 10:16:43: Fewer paired peaks (217) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 217 pairs to build model! INFO @ Tue, 16 Jun 2020 10:16:43: start model_add_line... INFO @ Tue, 16 Jun 2020 10:16:43: start X-correlation... INFO @ Tue, 16 Jun 2020 10:16:43: end of X-cor INFO @ Tue, 16 Jun 2020 10:16:43: #2 finished! INFO @ Tue, 16 Jun 2020 10:16:43: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 10:16:43: #2 alternative fragment length(s) may be 1,20,48,537,554 bps INFO @ Tue, 16 Jun 2020 10:16:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5702591/SRX5702591.20_model.r WARNING @ Tue, 16 Jun 2020 10:16:43: #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 10:16:43: #2 You may need to consider one of the other alternative d(s): 1,20,48,537,554 WARNING @ Tue, 16 Jun 2020 10:16:43: #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 10:16:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:16:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:16:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5702591/SRX5702591.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:16:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5702591/SRX5702591.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:16:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5702591/SRX5702591.10_summits.bed INFO @ Tue, 16 Jun 2020 10:16:54: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:17:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:17:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5702591/SRX5702591.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:17:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5702591/SRX5702591.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:17:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5702591/SRX5702591.20_summits.bed INFO @ Tue, 16 Jun 2020 10:17:42: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling