Job ID = 6458824 SRX = SRX5661474 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:41:57 prefetch.2.10.7: 1) Downloading 'SRR8874481'... 2020-06-21T12:41:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:48:41 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:48:41 prefetch.2.10.7: 1) 'SRR8874481' was downloaded successfully 2020-06-21T12:48:41 prefetch.2.10.7: 'SRR8874481' has 0 unresolved dependencies Read 45585242 spots for SRR8874481/SRR8874481.sra Written 45585242 spots for SRR8874481/SRR8874481.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: 00:16:38 45585242 reads; of these: 45585242 (100.00%) were unpaired; of these: 1934978 (4.24%) aligned 0 times 31148374 (68.33%) aligned exactly 1 time 12501890 (27.43%) aligned >1 times 95.76% overall alignment rate Time searching: 00:16:38 Overall time: 00:16:38 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 20 files... [bam_rmdupse_core] 9270915 / 43650264 = 0.2124 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 @ Sun, 21 Jun 2020 22:17:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5661474/SRX5661474.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5661474/SRX5661474.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5661474/SRX5661474.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5661474/SRX5661474.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 22:17:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:17:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:17:41: 1000000 INFO @ Sun, 21 Jun 2020 22:17:47: 2000000 INFO @ Sun, 21 Jun 2020 22:17:54: 3000000 INFO @ Sun, 21 Jun 2020 22:18:00: 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 @ Sun, 21 Jun 2020 22:18:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5661474/SRX5661474.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5661474/SRX5661474.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5661474/SRX5661474.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5661474/SRX5661474.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 22:18:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:18:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:18:07: 5000000 INFO @ Sun, 21 Jun 2020 22:18:09: 1000000 INFO @ Sun, 21 Jun 2020 22:18:14: 6000000 INFO @ Sun, 21 Jun 2020 22:18:15: 2000000 INFO @ Sun, 21 Jun 2020 22:18:21: 7000000 INFO @ Sun, 21 Jun 2020 22:18:21: 3000000 INFO @ Sun, 21 Jun 2020 22:18:28: 4000000 INFO @ Sun, 21 Jun 2020 22:18:28: 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 @ Sun, 21 Jun 2020 22:18:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5661474/SRX5661474.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5661474/SRX5661474.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5661474/SRX5661474.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5661474/SRX5661474.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 22:18:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:18:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:18:34: 5000000 INFO @ Sun, 21 Jun 2020 22:18:35: 9000000 INFO @ Sun, 21 Jun 2020 22:18:39: 1000000 INFO @ Sun, 21 Jun 2020 22:18:40: 6000000 INFO @ Sun, 21 Jun 2020 22:18:42: 10000000 INFO @ Sun, 21 Jun 2020 22:18:45: 2000000 INFO @ Sun, 21 Jun 2020 22:18:47: 7000000 INFO @ Sun, 21 Jun 2020 22:18:49: 11000000 INFO @ Sun, 21 Jun 2020 22:18:52: 3000000 INFO @ Sun, 21 Jun 2020 22:18:53: 8000000 INFO @ Sun, 21 Jun 2020 22:18:55: 12000000 INFO @ Sun, 21 Jun 2020 22:18:58: 4000000 INFO @ Sun, 21 Jun 2020 22:18:59: 9000000 INFO @ Sun, 21 Jun 2020 22:19:02: 13000000 INFO @ Sun, 21 Jun 2020 22:19:05: 5000000 INFO @ Sun, 21 Jun 2020 22:19:05: 10000000 INFO @ Sun, 21 Jun 2020 22:19:09: 14000000 INFO @ Sun, 21 Jun 2020 22:19:11: 6000000 INFO @ Sun, 21 Jun 2020 22:19:11: 11000000 INFO @ Sun, 21 Jun 2020 22:19:16: 15000000 INFO @ Sun, 21 Jun 2020 22:19:18: 12000000 INFO @ Sun, 21 Jun 2020 22:19:18: 7000000 INFO @ Sun, 21 Jun 2020 22:19:23: 16000000 INFO @ Sun, 21 Jun 2020 22:19:24: 13000000 INFO @ Sun, 21 Jun 2020 22:19:24: 8000000 INFO @ Sun, 21 Jun 2020 22:19:30: 17000000 INFO @ Sun, 21 Jun 2020 22:19:30: 14000000 INFO @ Sun, 21 Jun 2020 22:19:31: 9000000 INFO @ Sun, 21 Jun 2020 22:19:37: 18000000 INFO @ Sun, 21 Jun 2020 22:19:37: 15000000 INFO @ Sun, 21 Jun 2020 22:19:37: 10000000 INFO @ Sun, 21 Jun 2020 22:19:43: 16000000 INFO @ Sun, 21 Jun 2020 22:19:43: 11000000 INFO @ Sun, 21 Jun 2020 22:19:44: 19000000 INFO @ Sun, 21 Jun 2020 22:19:49: 17000000 INFO @ Sun, 21 Jun 2020 22:19:49: 12000000 INFO @ Sun, 21 Jun 2020 22:19:50: 20000000 INFO @ Sun, 21 Jun 2020 22:19:55: 18000000 INFO @ Sun, 21 Jun 2020 22:19:56: 13000000 INFO @ Sun, 21 Jun 2020 22:19:57: 21000000 INFO @ Sun, 21 Jun 2020 22:20:02: 19000000 INFO @ Sun, 21 Jun 2020 22:20:02: 14000000 INFO @ Sun, 21 Jun 2020 22:20:04: 22000000 INFO @ Sun, 21 Jun 2020 22:20:08: 20000000 INFO @ Sun, 21 Jun 2020 22:20:08: 15000000 INFO @ Sun, 21 Jun 2020 22:20:11: 23000000 INFO @ Sun, 21 Jun 2020 22:20:14: 21000000 INFO @ Sun, 21 Jun 2020 22:20:15: 16000000 INFO @ Sun, 21 Jun 2020 22:20:18: 24000000 INFO @ Sun, 21 Jun 2020 22:20:21: 22000000 INFO @ Sun, 21 Jun 2020 22:20:21: 17000000 INFO @ Sun, 21 Jun 2020 22:20:25: 25000000 INFO @ Sun, 21 Jun 2020 22:20:27: 23000000 INFO @ Sun, 21 Jun 2020 22:20:27: 18000000 INFO @ Sun, 21 Jun 2020 22:20:32: 26000000 INFO @ Sun, 21 Jun 2020 22:20:33: 24000000 INFO @ Sun, 21 Jun 2020 22:20:33: 19000000 INFO @ Sun, 21 Jun 2020 22:20:39: 27000000 INFO @ Sun, 21 Jun 2020 22:20:40: 20000000 INFO @ Sun, 21 Jun 2020 22:20:40: 25000000 INFO @ Sun, 21 Jun 2020 22:20:46: 21000000 INFO @ Sun, 21 Jun 2020 22:20:46: 26000000 INFO @ Sun, 21 Jun 2020 22:20:47: 28000000 INFO @ Sun, 21 Jun 2020 22:20:52: 22000000 INFO @ Sun, 21 Jun 2020 22:20:52: 27000000 INFO @ Sun, 21 Jun 2020 22:20:54: 29000000 INFO @ Sun, 21 Jun 2020 22:20:58: 23000000 INFO @ Sun, 21 Jun 2020 22:20:59: 28000000 INFO @ Sun, 21 Jun 2020 22:21:01: 30000000 INFO @ Sun, 21 Jun 2020 22:21:05: 24000000 INFO @ Sun, 21 Jun 2020 22:21:05: 29000000 INFO @ Sun, 21 Jun 2020 22:21:08: 31000000 INFO @ Sun, 21 Jun 2020 22:21:11: 25000000 INFO @ Sun, 21 Jun 2020 22:21:12: 30000000 INFO @ Sun, 21 Jun 2020 22:21:15: 32000000 INFO @ Sun, 21 Jun 2020 22:21:17: 26000000 INFO @ Sun, 21 Jun 2020 22:21:18: 31000000 INFO @ Sun, 21 Jun 2020 22:21:22: 33000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:21:24: 27000000 INFO @ Sun, 21 Jun 2020 22:21:24: 32000000 INFO @ Sun, 21 Jun 2020 22:21:29: 34000000 INFO @ Sun, 21 Jun 2020 22:21:30: 33000000 INFO @ Sun, 21 Jun 2020 22:21:31: 28000000 INFO @ Sun, 21 Jun 2020 22:21:32: #1 tag size is determined as 62 bps INFO @ Sun, 21 Jun 2020 22:21:32: #1 tag size = 62 INFO @ Sun, 21 Jun 2020 22:21:32: #1 total tags in treatment: 34379349 INFO @ Sun, 21 Jun 2020 22:21:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:21:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:21:33: #1 tags after filtering in treatment: 34379348 INFO @ Sun, 21 Jun 2020 22:21:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:21:33: #1 finished! INFO @ Sun, 21 Jun 2020 22:21:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:21:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:21:36: #2 number of paired peaks: 137 WARNING @ Sun, 21 Jun 2020 22:21:36: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Sun, 21 Jun 2020 22:21:36: start model_add_line... INFO @ Sun, 21 Jun 2020 22:21:36: start X-correlation... INFO @ Sun, 21 Jun 2020 22:21:36: end of X-cor INFO @ Sun, 21 Jun 2020 22:21:36: #2 finished! INFO @ Sun, 21 Jun 2020 22:21:36: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 22:21:36: #2 alternative fragment length(s) may be 2,38,53,588,590,596 bps INFO @ Sun, 21 Jun 2020 22:21:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5661474/SRX5661474.05_model.r WARNING @ Sun, 21 Jun 2020 22:21:36: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:21:36: #2 You may need to consider one of the other alternative d(s): 2,38,53,588,590,596 WARNING @ Sun, 21 Jun 2020 22:21:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:21:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:21:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:21:37: 34000000 INFO @ Sun, 21 Jun 2020 22:21:37: 29000000 INFO @ Sun, 21 Jun 2020 22:21:40: #1 tag size is determined as 62 bps INFO @ Sun, 21 Jun 2020 22:21:40: #1 tag size = 62 INFO @ Sun, 21 Jun 2020 22:21:40: #1 total tags in treatment: 34379349 INFO @ Sun, 21 Jun 2020 22:21:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:21:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:21:41: #1 tags after filtering in treatment: 34379348 INFO @ Sun, 21 Jun 2020 22:21:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:21:41: #1 finished! INFO @ Sun, 21 Jun 2020 22:21:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:21:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:21:43: #2 number of paired peaks: 137 WARNING @ Sun, 21 Jun 2020 22:21:43: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Sun, 21 Jun 2020 22:21:43: start model_add_line... INFO @ Sun, 21 Jun 2020 22:21:43: start X-correlation... INFO @ Sun, 21 Jun 2020 22:21:43: end of X-cor INFO @ Sun, 21 Jun 2020 22:21:43: #2 finished! INFO @ Sun, 21 Jun 2020 22:21:43: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 22:21:43: #2 alternative fragment length(s) may be 2,38,53,588,590,596 bps INFO @ Sun, 21 Jun 2020 22:21:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5661474/SRX5661474.10_model.r WARNING @ Sun, 21 Jun 2020 22:21:43: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:21:43: #2 You may need to consider one of the other alternative d(s): 2,38,53,588,590,596 WARNING @ Sun, 21 Jun 2020 22:21:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:21:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:21:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:21:43: 30000000 INFO @ Sun, 21 Jun 2020 22:21:49: 31000000 INFO @ Sun, 21 Jun 2020 22:21:54: 32000000 INFO @ Sun, 21 Jun 2020 22:22:00: 33000000 INFO @ Sun, 21 Jun 2020 22:22:06: 34000000 INFO @ Sun, 21 Jun 2020 22:22:09: #1 tag size is determined as 62 bps INFO @ Sun, 21 Jun 2020 22:22:09: #1 tag size = 62 INFO @ Sun, 21 Jun 2020 22:22:09: #1 total tags in treatment: 34379349 INFO @ Sun, 21 Jun 2020 22:22:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:22:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:22:09: #1 tags after filtering in treatment: 34379348 INFO @ Sun, 21 Jun 2020 22:22:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:22:09: #1 finished! INFO @ Sun, 21 Jun 2020 22:22:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:22:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:22:12: #2 number of paired peaks: 137 WARNING @ Sun, 21 Jun 2020 22:22:12: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Sun, 21 Jun 2020 22:22:12: start model_add_line... INFO @ Sun, 21 Jun 2020 22:22:12: start X-correlation... INFO @ Sun, 21 Jun 2020 22:22:12: end of X-cor INFO @ Sun, 21 Jun 2020 22:22:12: #2 finished! INFO @ Sun, 21 Jun 2020 22:22:12: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 22:22:12: #2 alternative fragment length(s) may be 2,38,53,588,590,596 bps INFO @ Sun, 21 Jun 2020 22:22:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5661474/SRX5661474.20_model.r WARNING @ Sun, 21 Jun 2020 22:22:12: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:22:12: #2 You may need to consider one of the other alternative d(s): 2,38,53,588,590,596 WARNING @ Sun, 21 Jun 2020 22:22:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:22:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:22:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:22:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:22:38: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:22:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5661474/SRX5661474.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:22:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5661474/SRX5661474.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:22:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5661474/SRX5661474.05_summits.bed INFO @ Sun, 21 Jun 2020 22:22:55: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:23:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5661474/SRX5661474.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:23:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5661474/SRX5661474.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:23:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5661474/SRX5661474.10_summits.bed INFO @ Sun, 21 Jun 2020 22:23:04: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:23:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:23:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5661474/SRX5661474.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:23:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5661474/SRX5661474.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:23:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5661474/SRX5661474.20_summits.bed INFO @ Sun, 21 Jun 2020 22:23:32: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling