Job ID = 6368068 SRX = SRX466531 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:55:03 prefetch.2.10.7: 1) Downloading 'SRR1163597'... 2020-06-15T23:55:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:57:11 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:57:11 prefetch.2.10.7: 1) 'SRR1163597' was downloaded successfully Read 30788149 spots for SRR1163597/SRR1163597.sra Written 30788149 spots for SRR1163597/SRR1163597.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: 00:05:55 30788149 reads; of these: 30788149 (100.00%) were unpaired; of these: 169822 (0.55%) aligned 0 times 25275342 (82.09%) aligned exactly 1 time 5342985 (17.35%) aligned >1 times 99.45% overall alignment rate Time searching: 00:05:55 Overall time: 00:05:55 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 8 files... [bam_rmdupse_core] 4711476 / 30618327 = 0.1539 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 09:11:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466531/SRX466531.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466531/SRX466531.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466531/SRX466531.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466531/SRX466531.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 09:11:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:11:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:11:11: 1000000 INFO @ Tue, 16 Jun 2020 09:11:17: 2000000 INFO @ Tue, 16 Jun 2020 09:11:24: 3000000 INFO @ Tue, 16 Jun 2020 09:11:30: 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 09:11:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466531/SRX466531.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466531/SRX466531.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466531/SRX466531.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466531/SRX466531.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 09:11:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:11:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:11:37: 5000000 INFO @ Tue, 16 Jun 2020 09:11:41: 1000000 INFO @ Tue, 16 Jun 2020 09:11:44: 6000000 INFO @ Tue, 16 Jun 2020 09:11:47: 2000000 INFO @ Tue, 16 Jun 2020 09:11:51: 7000000 INFO @ Tue, 16 Jun 2020 09:11:54: 3000000 INFO @ Tue, 16 Jun 2020 09:11:58: 8000000 INFO @ Tue, 16 Jun 2020 09:12:00: 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 09:12:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466531/SRX466531.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466531/SRX466531.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466531/SRX466531.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466531/SRX466531.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 09:12:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:12:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:12:05: 9000000 INFO @ Tue, 16 Jun 2020 09:12:06: 5000000 INFO @ Tue, 16 Jun 2020 09:12:12: 1000000 INFO @ Tue, 16 Jun 2020 09:12:12: 10000000 INFO @ Tue, 16 Jun 2020 09:12:13: 6000000 INFO @ Tue, 16 Jun 2020 09:12:19: 7000000 INFO @ Tue, 16 Jun 2020 09:12:19: 2000000 INFO @ Tue, 16 Jun 2020 09:12:20: 11000000 INFO @ Tue, 16 Jun 2020 09:12:26: 8000000 INFO @ Tue, 16 Jun 2020 09:12:27: 3000000 INFO @ Tue, 16 Jun 2020 09:12:27: 12000000 INFO @ Tue, 16 Jun 2020 09:12:32: 9000000 INFO @ Tue, 16 Jun 2020 09:12:34: 4000000 INFO @ Tue, 16 Jun 2020 09:12:34: 13000000 INFO @ Tue, 16 Jun 2020 09:12:38: 10000000 INFO @ Tue, 16 Jun 2020 09:12:41: 5000000 INFO @ Tue, 16 Jun 2020 09:12:42: 14000000 INFO @ Tue, 16 Jun 2020 09:12:44: 11000000 INFO @ Tue, 16 Jun 2020 09:12:49: 6000000 INFO @ Tue, 16 Jun 2020 09:12:49: 15000000 INFO @ Tue, 16 Jun 2020 09:12:51: 12000000 INFO @ Tue, 16 Jun 2020 09:12:56: 7000000 INFO @ Tue, 16 Jun 2020 09:12:57: 16000000 INFO @ Tue, 16 Jun 2020 09:12:57: 13000000 INFO @ Tue, 16 Jun 2020 09:13:03: 14000000 INFO @ Tue, 16 Jun 2020 09:13:03: 8000000 INFO @ Tue, 16 Jun 2020 09:13:04: 17000000 INFO @ Tue, 16 Jun 2020 09:13:09: 15000000 INFO @ Tue, 16 Jun 2020 09:13:11: 9000000 INFO @ Tue, 16 Jun 2020 09:13:11: 18000000 INFO @ Tue, 16 Jun 2020 09:13:15: 16000000 INFO @ Tue, 16 Jun 2020 09:13:18: 10000000 INFO @ Tue, 16 Jun 2020 09:13:19: 19000000 INFO @ Tue, 16 Jun 2020 09:13:22: 17000000 INFO @ Tue, 16 Jun 2020 09:13:25: 11000000 INFO @ Tue, 16 Jun 2020 09:13:26: 20000000 INFO @ Tue, 16 Jun 2020 09:13:28: 18000000 INFO @ Tue, 16 Jun 2020 09:13:32: 12000000 INFO @ Tue, 16 Jun 2020 09:13:34: 21000000 INFO @ Tue, 16 Jun 2020 09:13:34: 19000000 INFO @ Tue, 16 Jun 2020 09:13:40: 13000000 INFO @ Tue, 16 Jun 2020 09:13:40: 20000000 INFO @ Tue, 16 Jun 2020 09:13:41: 22000000 INFO @ Tue, 16 Jun 2020 09:13:46: 21000000 INFO @ Tue, 16 Jun 2020 09:13:47: 14000000 INFO @ Tue, 16 Jun 2020 09:13:48: 23000000 INFO @ Tue, 16 Jun 2020 09:13:52: 22000000 INFO @ Tue, 16 Jun 2020 09:13:55: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:13:56: 24000000 INFO @ Tue, 16 Jun 2020 09:13:58: 23000000 INFO @ Tue, 16 Jun 2020 09:14:02: 16000000 INFO @ Tue, 16 Jun 2020 09:14:03: 25000000 INFO @ Tue, 16 Jun 2020 09:14:04: 24000000 INFO @ Tue, 16 Jun 2020 09:14:09: 17000000 INFO @ Tue, 16 Jun 2020 09:14:10: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:14:10: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:14:10: #1 total tags in treatment: 25906851 INFO @ Tue, 16 Jun 2020 09:14:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:14:10: #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 09:14:10: 25000000 INFO @ Tue, 16 Jun 2020 09:14:10: #1 tags after filtering in treatment: 25906851 INFO @ Tue, 16 Jun 2020 09:14:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:14:10: #1 finished! INFO @ Tue, 16 Jun 2020 09:14:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:14:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:14:12: #2 number of paired peaks: 148 WARNING @ Tue, 16 Jun 2020 09:14:12: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Tue, 16 Jun 2020 09:14:12: start model_add_line... INFO @ Tue, 16 Jun 2020 09:14:12: start X-correlation... INFO @ Tue, 16 Jun 2020 09:14:12: end of X-cor INFO @ Tue, 16 Jun 2020 09:14:12: #2 finished! INFO @ Tue, 16 Jun 2020 09:14:12: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:14:12: #2 alternative fragment length(s) may be 1,32,512,591 bps INFO @ Tue, 16 Jun 2020 09:14:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466531/SRX466531.05_model.r WARNING @ Tue, 16 Jun 2020 09:14:12: #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 09:14:12: #2 You may need to consider one of the other alternative d(s): 1,32,512,591 WARNING @ Tue, 16 Jun 2020 09:14:12: #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 09:14:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:14:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:14:16: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:14:16: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:14:16: #1 total tags in treatment: 25906851 INFO @ Tue, 16 Jun 2020 09:14:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:14:16: #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 09:14:16: #1 tags after filtering in treatment: 25906851 INFO @ Tue, 16 Jun 2020 09:14:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:14:16: #1 finished! INFO @ Tue, 16 Jun 2020 09:14:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:14:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:14:16: 18000000 INFO @ Tue, 16 Jun 2020 09:14:18: #2 number of paired peaks: 148 WARNING @ Tue, 16 Jun 2020 09:14:18: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Tue, 16 Jun 2020 09:14:18: start model_add_line... INFO @ Tue, 16 Jun 2020 09:14:18: start X-correlation... INFO @ Tue, 16 Jun 2020 09:14:18: end of X-cor INFO @ Tue, 16 Jun 2020 09:14:18: #2 finished! INFO @ Tue, 16 Jun 2020 09:14:18: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:14:18: #2 alternative fragment length(s) may be 1,32,512,591 bps INFO @ Tue, 16 Jun 2020 09:14:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466531/SRX466531.10_model.r WARNING @ Tue, 16 Jun 2020 09:14:18: #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 09:14:18: #2 You may need to consider one of the other alternative d(s): 1,32,512,591 WARNING @ Tue, 16 Jun 2020 09:14:18: #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 09:14:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:14:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:14:23: 19000000 INFO @ Tue, 16 Jun 2020 09:14:30: 20000000 INFO @ Tue, 16 Jun 2020 09:14:36: 21000000 INFO @ Tue, 16 Jun 2020 09:14:43: 22000000 INFO @ Tue, 16 Jun 2020 09:14:49: 23000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:14:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:14:56: 24000000 INFO @ Tue, 16 Jun 2020 09:14:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:15:02: 25000000 INFO @ Tue, 16 Jun 2020 09:15:08: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:15:08: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:15:08: #1 total tags in treatment: 25906851 INFO @ Tue, 16 Jun 2020 09:15:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:15:08: #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 09:15:09: #1 tags after filtering in treatment: 25906851 INFO @ Tue, 16 Jun 2020 09:15:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:15:09: #1 finished! INFO @ Tue, 16 Jun 2020 09:15:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:15:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:15:11: #2 number of paired peaks: 148 WARNING @ Tue, 16 Jun 2020 09:15:11: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Tue, 16 Jun 2020 09:15:11: start model_add_line... INFO @ Tue, 16 Jun 2020 09:15:11: start X-correlation... INFO @ Tue, 16 Jun 2020 09:15:11: end of X-cor INFO @ Tue, 16 Jun 2020 09:15:11: #2 finished! INFO @ Tue, 16 Jun 2020 09:15:11: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:15:11: #2 alternative fragment length(s) may be 1,32,512,591 bps INFO @ Tue, 16 Jun 2020 09:15:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466531/SRX466531.20_model.r WARNING @ Tue, 16 Jun 2020 09:15:11: #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 09:15:11: #2 You may need to consider one of the other alternative d(s): 1,32,512,591 WARNING @ Tue, 16 Jun 2020 09:15:11: #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 09:15:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:15:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:15:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466531/SRX466531.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:15:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466531/SRX466531.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:15:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466531/SRX466531.05_summits.bed INFO @ Tue, 16 Jun 2020 09:15:11: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:15:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466531/SRX466531.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:15:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466531/SRX466531.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:15:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466531/SRX466531.10_summits.bed INFO @ Tue, 16 Jun 2020 09:15:14: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:15:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:16:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466531/SRX466531.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:16:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466531/SRX466531.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:16:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466531/SRX466531.20_summits.bed INFO @ Tue, 16 Jun 2020 09:16:08: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling