Job ID = 6368785 SRX = SRX5702592 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:30:27 prefetch.2.10.7: 1) Downloading 'SRR8921265'... 2020-06-16T00:30:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:31:40 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:31:40 prefetch.2.10.7: 'SRR8921265' is valid 2020-06-16T00:31:40 prefetch.2.10.7: 1) 'SRR8921265' was downloaded successfully 2020-06-16T00:31:40 prefetch.2.10.7: 'SRR8921265' has 0 unresolved dependencies Read 17078976 spots for SRR8921265/SRR8921265.sra Written 17078976 spots for SRR8921265/SRR8921265.sra 2020-06-16T00:32:45 prefetch.2.10.7: 1) Downloading 'SRR8921266'... 2020-06-16T00:32:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:37:32 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:37:32 prefetch.2.10.7: 1) 'SRR8921266' was downloaded successfully 2020-06-16T00:37:32 prefetch.2.10.7: 'SRR8921266' has 0 unresolved dependencies Read 56326135 spots for SRR8921266/SRR8921266.sra Written 56326135 spots for SRR8921266/SRR8921266.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: 00:16:53 73405111 reads; of these: 73405111 (100.00%) were unpaired; of these: 29862871 (40.68%) aligned 0 times 31881021 (43.43%) aligned exactly 1 time 11661219 (15.89%) aligned >1 times 59.32% overall alignment rate Time searching: 00:16:53 Overall time: 00:16:53 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 20 files... [bam_rmdupse_core] 15868876 / 43542240 = 0.3644 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 10:08:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5702592/SRX5702592.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5702592/SRX5702592.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5702592/SRX5702592.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5702592/SRX5702592.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 10:08:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:08:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:08:50: 1000000 INFO @ Tue, 16 Jun 2020 10:08:55: 2000000 INFO @ Tue, 16 Jun 2020 10:09:00: 3000000 INFO @ Tue, 16 Jun 2020 10:09:05: 4000000 INFO @ Tue, 16 Jun 2020 10:09:11: 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 10:09:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5702592/SRX5702592.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5702592/SRX5702592.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5702592/SRX5702592.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5702592/SRX5702592.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 10:09:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:09:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:09:16: 6000000 INFO @ Tue, 16 Jun 2020 10:09:20: 1000000 INFO @ Tue, 16 Jun 2020 10:09:21: 7000000 INFO @ Tue, 16 Jun 2020 10:09:26: 2000000 INFO @ Tue, 16 Jun 2020 10:09:27: 8000000 INFO @ Tue, 16 Jun 2020 10:09:32: 3000000 INFO @ Tue, 16 Jun 2020 10:09:32: 9000000 INFO @ Tue, 16 Jun 2020 10:09:38: 10000000 INFO @ Tue, 16 Jun 2020 10:09:38: 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 10:09:43: 11000000 INFO @ Tue, 16 Jun 2020 10:09:44: 5000000 INFO @ Tue, 16 Jun 2020 10:09:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5702592/SRX5702592.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5702592/SRX5702592.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5702592/SRX5702592.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5702592/SRX5702592.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 10:09:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:09:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:09:49: 12000000 INFO @ Tue, 16 Jun 2020 10:09:50: 6000000 INFO @ Tue, 16 Jun 2020 10:09:51: 1000000 INFO @ Tue, 16 Jun 2020 10:09:54: 13000000 INFO @ Tue, 16 Jun 2020 10:09:57: 7000000 INFO @ Tue, 16 Jun 2020 10:09:57: 2000000 INFO @ Tue, 16 Jun 2020 10:10:00: 14000000 INFO @ Tue, 16 Jun 2020 10:10:03: 8000000 INFO @ Tue, 16 Jun 2020 10:10:03: 3000000 INFO @ Tue, 16 Jun 2020 10:10:05: 15000000 INFO @ Tue, 16 Jun 2020 10:10:09: 9000000 INFO @ Tue, 16 Jun 2020 10:10:09: 4000000 INFO @ Tue, 16 Jun 2020 10:10:11: 16000000 INFO @ Tue, 16 Jun 2020 10:10:15: 10000000 INFO @ Tue, 16 Jun 2020 10:10:15: 5000000 INFO @ Tue, 16 Jun 2020 10:10:16: 17000000 INFO @ Tue, 16 Jun 2020 10:10:21: 11000000 INFO @ Tue, 16 Jun 2020 10:10:21: 6000000 INFO @ Tue, 16 Jun 2020 10:10:22: 18000000 INFO @ Tue, 16 Jun 2020 10:10:27: 19000000 INFO @ Tue, 16 Jun 2020 10:10:27: 12000000 INFO @ Tue, 16 Jun 2020 10:10:28: 7000000 INFO @ Tue, 16 Jun 2020 10:10:33: 20000000 INFO @ Tue, 16 Jun 2020 10:10:33: 13000000 INFO @ Tue, 16 Jun 2020 10:10:34: 8000000 INFO @ Tue, 16 Jun 2020 10:10:38: 21000000 INFO @ Tue, 16 Jun 2020 10:10:40: 14000000 INFO @ Tue, 16 Jun 2020 10:10:40: 9000000 INFO @ Tue, 16 Jun 2020 10:10:44: 22000000 INFO @ Tue, 16 Jun 2020 10:10:46: 15000000 INFO @ Tue, 16 Jun 2020 10:10:46: 10000000 INFO @ Tue, 16 Jun 2020 10:10:49: 23000000 INFO @ Tue, 16 Jun 2020 10:10:52: 11000000 INFO @ Tue, 16 Jun 2020 10:10:53: 16000000 INFO @ Tue, 16 Jun 2020 10:10:55: 24000000 INFO @ Tue, 16 Jun 2020 10:10:58: 12000000 INFO @ Tue, 16 Jun 2020 10:10:59: 17000000 INFO @ Tue, 16 Jun 2020 10:11:00: 25000000 INFO @ Tue, 16 Jun 2020 10:11:04: 13000000 INFO @ Tue, 16 Jun 2020 10:11:05: 18000000 INFO @ Tue, 16 Jun 2020 10:11:06: 26000000 INFO @ Tue, 16 Jun 2020 10:11:11: 14000000 INFO @ Tue, 16 Jun 2020 10:11:12: 19000000 INFO @ Tue, 16 Jun 2020 10:11:12: 27000000 INFO @ Tue, 16 Jun 2020 10:11:16: #1 tag size is determined as 60 bps INFO @ Tue, 16 Jun 2020 10:11:16: #1 tag size = 60 INFO @ Tue, 16 Jun 2020 10:11:16: #1 total tags in treatment: 27673364 INFO @ Tue, 16 Jun 2020 10:11:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:11:16: #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 10:11:17: #1 tags after filtering in treatment: 27673364 INFO @ Tue, 16 Jun 2020 10:11:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:11:17: #1 finished! INFO @ Tue, 16 Jun 2020 10:11:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:11:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:11:17: 15000000 INFO @ Tue, 16 Jun 2020 10:11:18: 20000000 INFO @ Tue, 16 Jun 2020 10:11:18: #2 number of paired peaks: 169 WARNING @ Tue, 16 Jun 2020 10:11:18: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Tue, 16 Jun 2020 10:11:18: start model_add_line... INFO @ Tue, 16 Jun 2020 10:11:19: start X-correlation... INFO @ Tue, 16 Jun 2020 10:11:19: end of X-cor INFO @ Tue, 16 Jun 2020 10:11:19: #2 finished! INFO @ Tue, 16 Jun 2020 10:11:19: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 10:11:19: #2 alternative fragment length(s) may be 1,39,567 bps INFO @ Tue, 16 Jun 2020 10:11:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5702592/SRX5702592.05_model.r WARNING @ Tue, 16 Jun 2020 10:11:19: #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 10:11:19: #2 You may need to consider one of the other alternative d(s): 1,39,567 WARNING @ Tue, 16 Jun 2020 10:11:19: #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 10:11:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:11:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:11:23: 16000000 INFO @ Tue, 16 Jun 2020 10:11:24: 21000000 INFO @ Tue, 16 Jun 2020 10:11:29: 17000000 INFO @ Tue, 16 Jun 2020 10:11:30: 22000000 INFO @ Tue, 16 Jun 2020 10:11:35: 18000000 INFO @ Tue, 16 Jun 2020 10:11:36: 23000000 INFO @ Tue, 16 Jun 2020 10:11:42: 19000000 INFO @ Tue, 16 Jun 2020 10:11:42: 24000000 INFO @ Tue, 16 Jun 2020 10:11:48: 20000000 INFO @ Tue, 16 Jun 2020 10:11:48: 25000000 INFO @ Tue, 16 Jun 2020 10:11:54: 21000000 INFO @ Tue, 16 Jun 2020 10:11:55: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:11:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:12:01: 27000000 INFO @ Tue, 16 Jun 2020 10:12:01: 22000000 INFO @ Tue, 16 Jun 2020 10:12:06: #1 tag size is determined as 60 bps INFO @ Tue, 16 Jun 2020 10:12:06: #1 tag size = 60 INFO @ Tue, 16 Jun 2020 10:12:06: #1 total tags in treatment: 27673364 INFO @ Tue, 16 Jun 2020 10:12:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:12:06: #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 10:12:06: #1 tags after filtering in treatment: 27673364 INFO @ Tue, 16 Jun 2020 10:12:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:12:06: #1 finished! INFO @ Tue, 16 Jun 2020 10:12:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:12:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:12:08: #2 number of paired peaks: 169 WARNING @ Tue, 16 Jun 2020 10:12:08: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Tue, 16 Jun 2020 10:12:08: start model_add_line... INFO @ Tue, 16 Jun 2020 10:12:08: 23000000 INFO @ Tue, 16 Jun 2020 10:12:08: start X-correlation... INFO @ Tue, 16 Jun 2020 10:12:08: end of X-cor INFO @ Tue, 16 Jun 2020 10:12:08: #2 finished! INFO @ Tue, 16 Jun 2020 10:12:08: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 10:12:08: #2 alternative fragment length(s) may be 1,39,567 bps INFO @ Tue, 16 Jun 2020 10:12:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5702592/SRX5702592.10_model.r WARNING @ Tue, 16 Jun 2020 10:12:08: #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 10:12:08: #2 You may need to consider one of the other alternative d(s): 1,39,567 WARNING @ Tue, 16 Jun 2020 10:12:08: #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 10:12:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:12:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:12:15: 24000000 INFO @ Tue, 16 Jun 2020 10:12:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5702592/SRX5702592.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:12:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5702592/SRX5702592.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:12:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5702592/SRX5702592.05_summits.bed INFO @ Tue, 16 Jun 2020 10:12:18: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:12:21: 25000000 INFO @ Tue, 16 Jun 2020 10:12:28: 26000000 INFO @ Tue, 16 Jun 2020 10:12:34: 27000000 INFO @ Tue, 16 Jun 2020 10:12:39: #1 tag size is determined as 60 bps INFO @ Tue, 16 Jun 2020 10:12:39: #1 tag size = 60 INFO @ Tue, 16 Jun 2020 10:12:39: #1 total tags in treatment: 27673364 INFO @ Tue, 16 Jun 2020 10:12:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:12:39: #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 10:12:39: #1 tags after filtering in treatment: 27673364 INFO @ Tue, 16 Jun 2020 10:12:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:12:39: #1 finished! INFO @ Tue, 16 Jun 2020 10:12:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:12:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:12:41: #2 number of paired peaks: 169 WARNING @ Tue, 16 Jun 2020 10:12:41: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Tue, 16 Jun 2020 10:12:41: start model_add_line... INFO @ Tue, 16 Jun 2020 10:12:41: start X-correlation... INFO @ Tue, 16 Jun 2020 10:12:41: end of X-cor INFO @ Tue, 16 Jun 2020 10:12:41: #2 finished! INFO @ Tue, 16 Jun 2020 10:12:41: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 10:12:41: #2 alternative fragment length(s) may be 1,39,567 bps INFO @ Tue, 16 Jun 2020 10:12:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5702592/SRX5702592.20_model.r WARNING @ Tue, 16 Jun 2020 10:12:41: #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 10:12:41: #2 You may need to consider one of the other alternative d(s): 1,39,567 WARNING @ Tue, 16 Jun 2020 10:12:41: #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 10:12:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:12:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:12:49: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:13:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5702592/SRX5702592.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:13:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5702592/SRX5702592.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:13:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5702592/SRX5702592.10_summits.bed INFO @ Tue, 16 Jun 2020 10:13:08: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:13:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:13:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5702592/SRX5702592.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:13:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5702592/SRX5702592.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:13:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5702592/SRX5702592.20_summits.bed INFO @ Tue, 16 Jun 2020 10:13:42: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling