Job ID = 2590159 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,970,231 reads read : 22,970,231 reads written : 22,970,231 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:05:19 22970231 reads; of these: 22970231 (100.00%) were unpaired; of these: 2517640 (10.96%) aligned 0 times 16805683 (73.16%) aligned exactly 1 time 3646908 (15.88%) aligned >1 times 89.04% overall alignment rate Time searching: 00:05:19 Overall time: 00:05:19 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 12 files... [bam_rmdupse_core] 2297137 / 20452591 = 0.1123 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Mon, 12 Aug 2019 20:10:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495029/SRX495029.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495029/SRX495029.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495029/SRX495029.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495029/SRX495029.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 @ Mon, 12 Aug 2019 20:10:07: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:10:07: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:10:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495029/SRX495029.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495029/SRX495029.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495029/SRX495029.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495029/SRX495029.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 @ Mon, 12 Aug 2019 20:10:08: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:10:08: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:10:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495029/SRX495029.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495029/SRX495029.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495029/SRX495029.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495029/SRX495029.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 @ Mon, 12 Aug 2019 20:10:09: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:10:09: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:10:15: 1000000 INFO @ Mon, 12 Aug 2019 20:10:15: 1000000 INFO @ Mon, 12 Aug 2019 20:10:17: 1000000 INFO @ Mon, 12 Aug 2019 20:10:22: 2000000 INFO @ Mon, 12 Aug 2019 20:10:23: 2000000 INFO @ Mon, 12 Aug 2019 20:10:25: 2000000 INFO @ Mon, 12 Aug 2019 20:10:29: 3000000 INFO @ Mon, 12 Aug 2019 20:10:31: 3000000 INFO @ Mon, 12 Aug 2019 20:10:32: 3000000 INFO @ Mon, 12 Aug 2019 20:10:36: 4000000 INFO @ Mon, 12 Aug 2019 20:10:39: 4000000 INFO @ Mon, 12 Aug 2019 20:10:40: 4000000 INFO @ Mon, 12 Aug 2019 20:10:44: 5000000 INFO @ Mon, 12 Aug 2019 20:10:47: 5000000 INFO @ Mon, 12 Aug 2019 20:10:48: 5000000 INFO @ Mon, 12 Aug 2019 20:10:51: 6000000 INFO @ Mon, 12 Aug 2019 20:10:55: 6000000 INFO @ Mon, 12 Aug 2019 20:10:56: 6000000 INFO @ Mon, 12 Aug 2019 20:10:58: 7000000 INFO @ Mon, 12 Aug 2019 20:11:04: 7000000 INFO @ Mon, 12 Aug 2019 20:11:04: 7000000 INFO @ Mon, 12 Aug 2019 20:11:05: 8000000 INFO @ Mon, 12 Aug 2019 20:11:12: 9000000 INFO @ Mon, 12 Aug 2019 20:11:12: 8000000 INFO @ Mon, 12 Aug 2019 20:11:12: 8000000 INFO @ Mon, 12 Aug 2019 20:11:19: 10000000 INFO @ Mon, 12 Aug 2019 20:11:20: 9000000 INFO @ Mon, 12 Aug 2019 20:11:20: 9000000 INFO @ Mon, 12 Aug 2019 20:11:26: 11000000 INFO @ Mon, 12 Aug 2019 20:11:28: 10000000 INFO @ Mon, 12 Aug 2019 20:11:28: 10000000 INFO @ Mon, 12 Aug 2019 20:11:33: 12000000 INFO @ Mon, 12 Aug 2019 20:11:36: 11000000 INFO @ Mon, 12 Aug 2019 20:11:37: 11000000 INFO @ Mon, 12 Aug 2019 20:11:40: 13000000 INFO @ Mon, 12 Aug 2019 20:11:44: 12000000 INFO @ Mon, 12 Aug 2019 20:11:45: 12000000 INFO @ Mon, 12 Aug 2019 20:11:47: 14000000 INFO @ Mon, 12 Aug 2019 20:11:51: 13000000 INFO @ Mon, 12 Aug 2019 20:11:53: 13000000 INFO @ Mon, 12 Aug 2019 20:11:54: 15000000 INFO @ Mon, 12 Aug 2019 20:11:59: 14000000 INFO @ Mon, 12 Aug 2019 20:12:00: 14000000 INFO @ Mon, 12 Aug 2019 20:12:01: 16000000 INFO @ Mon, 12 Aug 2019 20:12:07: 15000000 INFO @ Mon, 12 Aug 2019 20:12:08: 17000000 INFO @ Mon, 12 Aug 2019 20:12:08: 15000000 INFO @ Mon, 12 Aug 2019 20:12:15: 16000000 INFO @ Mon, 12 Aug 2019 20:12:15: 18000000 INFO @ Mon, 12 Aug 2019 20:12:16: 16000000 INFO @ Mon, 12 Aug 2019 20:12:17: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:12:17: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:12:17: #1 total tags in treatment: 18155454 INFO @ Mon, 12 Aug 2019 20:12:17: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:12:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:12:17: #1 tags after filtering in treatment: 18155454 INFO @ Mon, 12 Aug 2019 20:12:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:12:17: #1 finished! INFO @ Mon, 12 Aug 2019 20:12:17: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:12:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:12:18: #2 number of paired peaks: 263 WARNING @ Mon, 12 Aug 2019 20:12:18: Fewer paired peaks (263) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 263 pairs to build model! INFO @ Mon, 12 Aug 2019 20:12:18: start model_add_line... INFO @ Mon, 12 Aug 2019 20:12:19: start X-correlation... INFO @ Mon, 12 Aug 2019 20:12:19: end of X-cor INFO @ Mon, 12 Aug 2019 20:12:19: #2 finished! INFO @ Mon, 12 Aug 2019 20:12:19: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 20:12:19: #2 alternative fragment length(s) may be 1,29,579 bps INFO @ Mon, 12 Aug 2019 20:12:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495029/SRX495029.10_model.r WARNING @ Mon, 12 Aug 2019 20:12:19: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:12:19: #2 You may need to consider one of the other alternative d(s): 1,29,579 WARNING @ Mon, 12 Aug 2019 20:12:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:12:19: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:12:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:12:22: 17000000 INFO @ Mon, 12 Aug 2019 20:12:24: 17000000 INFO @ Mon, 12 Aug 2019 20:12:30: 18000000 INFO @ Mon, 12 Aug 2019 20:12:31: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:12:31: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:12:31: #1 total tags in treatment: 18155454 INFO @ Mon, 12 Aug 2019 20:12:31: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:12:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:12:32: #1 tags after filtering in treatment: 18155454 INFO @ Mon, 12 Aug 2019 20:12:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:12:32: #1 finished! INFO @ Mon, 12 Aug 2019 20:12:32: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:12:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:12:32: 18000000 INFO @ Mon, 12 Aug 2019 20:12:33: #2 number of paired peaks: 263 WARNING @ Mon, 12 Aug 2019 20:12:33: Fewer paired peaks (263) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 263 pairs to build model! INFO @ Mon, 12 Aug 2019 20:12:33: start model_add_line... INFO @ Mon, 12 Aug 2019 20:12:33: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:12:33: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:12:33: #1 total tags in treatment: 18155454 INFO @ Mon, 12 Aug 2019 20:12:33: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:12:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:12:34: start X-correlation... INFO @ Mon, 12 Aug 2019 20:12:34: end of X-cor INFO @ Mon, 12 Aug 2019 20:12:34: #2 finished! INFO @ Mon, 12 Aug 2019 20:12:34: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 20:12:34: #2 alternative fragment length(s) may be 1,29,579 bps INFO @ Mon, 12 Aug 2019 20:12:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495029/SRX495029.20_model.r WARNING @ Mon, 12 Aug 2019 20:12:34: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:12:34: #2 You may need to consider one of the other alternative d(s): 1,29,579 WARNING @ Mon, 12 Aug 2019 20:12:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:12:34: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:12:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:12:34: #1 tags after filtering in treatment: 18155454 INFO @ Mon, 12 Aug 2019 20:12:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:12:34: #1 finished! INFO @ Mon, 12 Aug 2019 20:12:34: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:12:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:12:35: #2 number of paired peaks: 263 WARNING @ Mon, 12 Aug 2019 20:12:35: Fewer paired peaks (263) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 263 pairs to build model! INFO @ Mon, 12 Aug 2019 20:12:35: start model_add_line... INFO @ Mon, 12 Aug 2019 20:12:36: start X-correlation... INFO @ Mon, 12 Aug 2019 20:12:36: end of X-cor INFO @ Mon, 12 Aug 2019 20:12:36: #2 finished! INFO @ Mon, 12 Aug 2019 20:12:36: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 20:12:36: #2 alternative fragment length(s) may be 1,29,579 bps INFO @ Mon, 12 Aug 2019 20:12:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495029/SRX495029.05_model.r WARNING @ Mon, 12 Aug 2019 20:12:36: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:12:36: #2 You may need to consider one of the other alternative d(s): 1,29,579 WARNING @ Mon, 12 Aug 2019 20:12:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:12:36: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:12:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:12:59: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:13:14: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:13:16: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:13:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495029/SRX495029.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:13:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495029/SRX495029.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:13:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495029/SRX495029.10_summits.bed INFO @ Mon, 12 Aug 2019 20:13:17: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:13:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495029/SRX495029.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:13:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495029/SRX495029.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:13:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495029/SRX495029.20_summits.bed INFO @ Mon, 12 Aug 2019 20:13:32: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:13:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495029/SRX495029.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:13:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495029/SRX495029.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:13:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495029/SRX495029.05_summits.bed INFO @ Mon, 12 Aug 2019 20:13:34: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。