Job ID = 6507945 SRX = SRX495105 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T14:19:27 prefetch.2.10.7: 1) Downloading 'SRR1198637'... 2020-06-26T14:19:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:23:03 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:23:03 prefetch.2.10.7: 1) 'SRR1198637' was downloaded successfully Read 32317902 spots for SRR1198637/SRR1198637.sra Written 32317902 spots for SRR1198637/SRR1198637.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: 00:11:04 32317902 reads; of these: 32317902 (100.00%) were unpaired; of these: 1918969 (5.94%) aligned 0 times 24975550 (77.28%) aligned exactly 1 time 5423383 (16.78%) aligned >1 times 94.06% overall alignment rate Time searching: 00:11:04 Overall time: 00:11:04 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 16 files... [bam_rmdupse_core] 5471963 / 30398933 = 0.1800 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 @ Fri, 26 Jun 2020 23:46:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495105/SRX495105.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495105/SRX495105.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495105/SRX495105.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495105/SRX495105.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 @ Fri, 26 Jun 2020 23:46:07: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:46:07: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:46:14: 1000000 INFO @ Fri, 26 Jun 2020 23:46:20: 2000000 INFO @ Fri, 26 Jun 2020 23:46:26: 3000000 INFO @ Fri, 26 Jun 2020 23:46:32: 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 @ Fri, 26 Jun 2020 23:46:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495105/SRX495105.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495105/SRX495105.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495105/SRX495105.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495105/SRX495105.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 @ Fri, 26 Jun 2020 23:46:36: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:46:36: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:46:39: 5000000 INFO @ Fri, 26 Jun 2020 23:46:43: 1000000 INFO @ Fri, 26 Jun 2020 23:46:46: 6000000 INFO @ Fri, 26 Jun 2020 23:46:51: 2000000 INFO @ Fri, 26 Jun 2020 23:46:53: 7000000 INFO @ Fri, 26 Jun 2020 23:46:58: 3000000 INFO @ Fri, 26 Jun 2020 23:47:00: 8000000 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 @ Fri, 26 Jun 2020 23:47:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495105/SRX495105.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495105/SRX495105.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495105/SRX495105.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495105/SRX495105.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 @ Fri, 26 Jun 2020 23:47:06: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:47:06: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:47:06: 4000000 INFO @ Fri, 26 Jun 2020 23:47:07: 9000000 INFO @ Fri, 26 Jun 2020 23:47:13: 1000000 INFO @ Fri, 26 Jun 2020 23:47:13: 5000000 INFO @ Fri, 26 Jun 2020 23:47:14: 10000000 INFO @ Fri, 26 Jun 2020 23:47:21: 2000000 INFO @ Fri, 26 Jun 2020 23:47:21: 6000000 INFO @ Fri, 26 Jun 2020 23:47:22: 11000000 INFO @ Fri, 26 Jun 2020 23:47:29: 3000000 INFO @ Fri, 26 Jun 2020 23:47:29: 7000000 INFO @ Fri, 26 Jun 2020 23:47:31: 12000000 INFO @ Fri, 26 Jun 2020 23:47:36: 4000000 INFO @ Fri, 26 Jun 2020 23:47:37: 8000000 INFO @ Fri, 26 Jun 2020 23:47:39: 13000000 INFO @ Fri, 26 Jun 2020 23:47:44: 5000000 INFO @ Fri, 26 Jun 2020 23:47:44: 9000000 INFO @ Fri, 26 Jun 2020 23:47:47: 14000000 INFO @ Fri, 26 Jun 2020 23:47:52: 6000000 INFO @ Fri, 26 Jun 2020 23:47:52: 10000000 INFO @ Fri, 26 Jun 2020 23:47:55: 15000000 INFO @ Fri, 26 Jun 2020 23:48:00: 7000000 INFO @ Fri, 26 Jun 2020 23:48:01: 11000000 INFO @ Fri, 26 Jun 2020 23:48:03: 16000000 INFO @ Fri, 26 Jun 2020 23:48:08: 8000000 INFO @ Fri, 26 Jun 2020 23:48:09: 12000000 INFO @ Fri, 26 Jun 2020 23:48:11: 17000000 INFO @ Fri, 26 Jun 2020 23:48:16: 9000000 INFO @ Fri, 26 Jun 2020 23:48:16: 13000000 INFO @ Fri, 26 Jun 2020 23:48:20: 18000000 INFO @ Fri, 26 Jun 2020 23:48:24: 10000000 INFO @ Fri, 26 Jun 2020 23:48:24: 14000000 INFO @ Fri, 26 Jun 2020 23:48:28: 19000000 INFO @ Fri, 26 Jun 2020 23:48:32: 11000000 INFO @ Fri, 26 Jun 2020 23:48:32: 15000000 INFO @ Fri, 26 Jun 2020 23:48:36: 20000000 INFO @ Fri, 26 Jun 2020 23:48:40: 12000000 INFO @ Fri, 26 Jun 2020 23:48:41: 16000000 INFO @ Fri, 26 Jun 2020 23:48:44: 21000000 INFO @ Fri, 26 Jun 2020 23:48:49: 13000000 INFO @ Fri, 26 Jun 2020 23:48:50: 17000000 INFO @ Fri, 26 Jun 2020 23:48:52: 22000000 INFO @ Fri, 26 Jun 2020 23:48:58: 14000000 INFO @ Fri, 26 Jun 2020 23:48:58: 18000000 INFO @ Fri, 26 Jun 2020 23:49:00: 23000000 INFO @ Fri, 26 Jun 2020 23:49:06: 15000000 INFO @ Fri, 26 Jun 2020 23:49:07: 19000000 INFO @ Fri, 26 Jun 2020 23:49:08: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:49:14: 16000000 INFO @ Fri, 26 Jun 2020 23:49:16: 20000000 INFO @ Fri, 26 Jun 2020 23:49:16: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:49:16: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:49:16: #1 total tags in treatment: 24926970 INFO @ Fri, 26 Jun 2020 23:49:16: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:49:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:49:16: #1 tags after filtering in treatment: 24926970 INFO @ Fri, 26 Jun 2020 23:49:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:49:16: #1 finished! INFO @ Fri, 26 Jun 2020 23:49:16: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:49:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:49:18: #2 number of paired peaks: 136 WARNING @ Fri, 26 Jun 2020 23:49:18: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Fri, 26 Jun 2020 23:49:18: start model_add_line... INFO @ Fri, 26 Jun 2020 23:49:18: start X-correlation... INFO @ Fri, 26 Jun 2020 23:49:18: end of X-cor INFO @ Fri, 26 Jun 2020 23:49:18: #2 finished! INFO @ Fri, 26 Jun 2020 23:49:18: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 23:49:18: #2 alternative fragment length(s) may be 1,36,45,186,211 bps INFO @ Fri, 26 Jun 2020 23:49:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495105/SRX495105.05_model.r WARNING @ Fri, 26 Jun 2020 23:49:18: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:49:18: #2 You may need to consider one of the other alternative d(s): 1,36,45,186,211 WARNING @ Fri, 26 Jun 2020 23:49:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:49:18: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:49:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:49:22: 17000000 INFO @ Fri, 26 Jun 2020 23:49:24: 21000000 INFO @ Fri, 26 Jun 2020 23:49:30: 18000000 INFO @ Fri, 26 Jun 2020 23:49:32: 22000000 INFO @ Fri, 26 Jun 2020 23:49:38: 19000000 INFO @ Fri, 26 Jun 2020 23:49:40: 23000000 INFO @ Fri, 26 Jun 2020 23:49:45: 20000000 INFO @ Fri, 26 Jun 2020 23:49:48: 24000000 INFO @ Fri, 26 Jun 2020 23:49:53: 21000000 INFO @ Fri, 26 Jun 2020 23:49:55: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:49:55: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:49:55: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:49:55: #1 total tags in treatment: 24926970 INFO @ Fri, 26 Jun 2020 23:49:55: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:49:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:49:55: #1 tags after filtering in treatment: 24926970 INFO @ Fri, 26 Jun 2020 23:49:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:49:55: #1 finished! INFO @ Fri, 26 Jun 2020 23:49:55: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:49:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:49:57: #2 number of paired peaks: 136 WARNING @ Fri, 26 Jun 2020 23:49:57: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Fri, 26 Jun 2020 23:49:57: start model_add_line... INFO @ Fri, 26 Jun 2020 23:49:57: start X-correlation... INFO @ Fri, 26 Jun 2020 23:49:57: end of X-cor INFO @ Fri, 26 Jun 2020 23:49:57: #2 finished! INFO @ Fri, 26 Jun 2020 23:49:57: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 23:49:57: #2 alternative fragment length(s) may be 1,36,45,186,211 bps INFO @ Fri, 26 Jun 2020 23:49:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495105/SRX495105.10_model.r WARNING @ Fri, 26 Jun 2020 23:49:57: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:49:57: #2 You may need to consider one of the other alternative d(s): 1,36,45,186,211 WARNING @ Fri, 26 Jun 2020 23:49:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:49:57: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:49:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:50:00: 22000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:50:07: 23000000 INFO @ Fri, 26 Jun 2020 23:50:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495105/SRX495105.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:50:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495105/SRX495105.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:50:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495105/SRX495105.05_summits.bed INFO @ Fri, 26 Jun 2020 23:50:12: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:50:13: 24000000 INFO @ Fri, 26 Jun 2020 23:50:19: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:50:19: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:50:19: #1 total tags in treatment: 24926970 INFO @ Fri, 26 Jun 2020 23:50:19: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:50:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:50:19: #1 tags after filtering in treatment: 24926970 INFO @ Fri, 26 Jun 2020 23:50:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:50:19: #1 finished! INFO @ Fri, 26 Jun 2020 23:50:19: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:50:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:50:21: #2 number of paired peaks: 136 WARNING @ Fri, 26 Jun 2020 23:50:21: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Fri, 26 Jun 2020 23:50:21: start model_add_line... INFO @ Fri, 26 Jun 2020 23:50:21: start X-correlation... INFO @ Fri, 26 Jun 2020 23:50:21: end of X-cor INFO @ Fri, 26 Jun 2020 23:50:21: #2 finished! INFO @ Fri, 26 Jun 2020 23:50:21: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 23:50:21: #2 alternative fragment length(s) may be 1,36,45,186,211 bps INFO @ Fri, 26 Jun 2020 23:50:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495105/SRX495105.20_model.r WARNING @ Fri, 26 Jun 2020 23:50:21: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:50:21: #2 You may need to consider one of the other alternative d(s): 1,36,45,186,211 WARNING @ Fri, 26 Jun 2020 23:50:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:50:21: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:50:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:50:35: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:50:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495105/SRX495105.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:50:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495105/SRX495105.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:50:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495105/SRX495105.10_summits.bed INFO @ Fri, 26 Jun 2020 23:50:53: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:50:59: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:51:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495105/SRX495105.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:51:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495105/SRX495105.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:51:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495105/SRX495105.20_summits.bed INFO @ Fri, 26 Jun 2020 23:51:17: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling