Job ID = 1293095 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,333,805 reads read : 20,333,805 reads written : 20,333,805 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:04:05 20333805 reads; of these: 20333805 (100.00%) were unpaired; of these: 243355 (1.20%) aligned 0 times 16211289 (79.73%) aligned exactly 1 time 3879161 (19.08%) aligned >1 times 98.80% overall alignment rate Time searching: 00:04:05 Overall time: 00:04:05 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] 2866846 / 20090450 = 0.1427 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 @ Sun, 02 Jun 2019 22:04:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529209/SRX529209.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529209/SRX529209.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529209/SRX529209.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529209/SRX529209.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 @ Sun, 02 Jun 2019 22:04:57: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:04:57: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:04:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529209/SRX529209.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529209/SRX529209.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529209/SRX529209.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529209/SRX529209.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 @ Sun, 02 Jun 2019 22:04:57: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:04:57: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:04:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529209/SRX529209.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529209/SRX529209.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529209/SRX529209.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529209/SRX529209.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 @ Sun, 02 Jun 2019 22:04:57: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:04:57: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:05:05: 1000000 INFO @ Sun, 02 Jun 2019 22:05:05: 1000000 INFO @ Sun, 02 Jun 2019 22:05:06: 1000000 INFO @ Sun, 02 Jun 2019 22:05:13: 2000000 INFO @ Sun, 02 Jun 2019 22:05:13: 2000000 INFO @ Sun, 02 Jun 2019 22:05:15: 2000000 INFO @ Sun, 02 Jun 2019 22:05:21: 3000000 INFO @ Sun, 02 Jun 2019 22:05:21: 3000000 INFO @ Sun, 02 Jun 2019 22:05:25: 3000000 INFO @ Sun, 02 Jun 2019 22:05:29: 4000000 INFO @ Sun, 02 Jun 2019 22:05:29: 4000000 INFO @ Sun, 02 Jun 2019 22:05:34: 4000000 INFO @ Sun, 02 Jun 2019 22:05:36: 5000000 INFO @ Sun, 02 Jun 2019 22:05:37: 5000000 INFO @ Sun, 02 Jun 2019 22:05:43: 5000000 INFO @ Sun, 02 Jun 2019 22:05:44: 6000000 INFO @ Sun, 02 Jun 2019 22:05:44: 6000000 INFO @ Sun, 02 Jun 2019 22:05:52: 7000000 INFO @ Sun, 02 Jun 2019 22:05:52: 6000000 INFO @ Sun, 02 Jun 2019 22:05:53: 7000000 INFO @ Sun, 02 Jun 2019 22:05:59: 8000000 INFO @ Sun, 02 Jun 2019 22:06:00: 8000000 INFO @ Sun, 02 Jun 2019 22:06:01: 7000000 INFO @ Sun, 02 Jun 2019 22:06:07: 9000000 INFO @ Sun, 02 Jun 2019 22:06:08: 9000000 INFO @ Sun, 02 Jun 2019 22:06:10: 8000000 INFO @ Sun, 02 Jun 2019 22:06:14: 10000000 INFO @ Sun, 02 Jun 2019 22:06:16: 10000000 INFO @ Sun, 02 Jun 2019 22:06:18: 9000000 INFO @ Sun, 02 Jun 2019 22:06:22: 11000000 INFO @ Sun, 02 Jun 2019 22:06:23: 11000000 INFO @ Sun, 02 Jun 2019 22:06:27: 10000000 INFO @ Sun, 02 Jun 2019 22:06:29: 12000000 INFO @ Sun, 02 Jun 2019 22:06:31: 12000000 INFO @ Sun, 02 Jun 2019 22:06:36: 11000000 INFO @ Sun, 02 Jun 2019 22:06:37: 13000000 INFO @ Sun, 02 Jun 2019 22:06:39: 13000000 INFO @ Sun, 02 Jun 2019 22:06:44: 14000000 INFO @ Sun, 02 Jun 2019 22:06:45: 12000000 INFO @ Sun, 02 Jun 2019 22:06:46: 14000000 INFO @ Sun, 02 Jun 2019 22:06:52: 15000000 INFO @ Sun, 02 Jun 2019 22:06:53: 13000000 INFO @ Sun, 02 Jun 2019 22:06:54: 15000000 INFO @ Sun, 02 Jun 2019 22:06:59: 16000000 INFO @ Sun, 02 Jun 2019 22:07:02: 16000000 INFO @ Sun, 02 Jun 2019 22:07:02: 14000000 INFO @ Sun, 02 Jun 2019 22:07:07: 17000000 INFO @ Sun, 02 Jun 2019 22:07:09: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 22:07:09: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 22:07:09: #1 total tags in treatment: 17223604 INFO @ Sun, 02 Jun 2019 22:07:09: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:07:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 22:07:09: #1 tags after filtering in treatment: 17223604 INFO @ Sun, 02 Jun 2019 22:07:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:07:09: #1 finished! INFO @ Sun, 02 Jun 2019 22:07:09: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:07:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:07:09: 17000000 INFO @ Sun, 02 Jun 2019 22:07:10: 15000000 INFO @ Sun, 02 Jun 2019 22:07:11: #2 number of paired peaks: 209 WARNING @ Sun, 02 Jun 2019 22:07:11: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Sun, 02 Jun 2019 22:07:11: start model_add_line... INFO @ Sun, 02 Jun 2019 22:07:11: start X-correlation... INFO @ Sun, 02 Jun 2019 22:07:11: end of X-cor INFO @ Sun, 02 Jun 2019 22:07:11: #2 finished! INFO @ Sun, 02 Jun 2019 22:07:11: #2 predicted fragment length is 2 bps INFO @ Sun, 02 Jun 2019 22:07:11: #2 alternative fragment length(s) may be 2,15,37,489,515,538,574 bps INFO @ Sun, 02 Jun 2019 22:07:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529209/SRX529209.20_model.r WARNING @ Sun, 02 Jun 2019 22:07:11: #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, 02 Jun 2019 22:07:11: #2 You may need to consider one of the other alternative d(s): 2,15,37,489,515,538,574 WARNING @ Sun, 02 Jun 2019 22:07:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 22:07:11: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:07:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:07:11: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 22:07:11: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 22:07:11: #1 total tags in treatment: 17223604 INFO @ Sun, 02 Jun 2019 22:07:11: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:07:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 22:07:11: #1 tags after filtering in treatment: 17223604 INFO @ Sun, 02 Jun 2019 22:07:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:07:11: #1 finished! INFO @ Sun, 02 Jun 2019 22:07:11: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:07:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:07:13: #2 number of paired peaks: 209 WARNING @ Sun, 02 Jun 2019 22:07:13: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Sun, 02 Jun 2019 22:07:13: start model_add_line... INFO @ Sun, 02 Jun 2019 22:07:13: start X-correlation... INFO @ Sun, 02 Jun 2019 22:07:13: end of X-cor INFO @ Sun, 02 Jun 2019 22:07:13: #2 finished! INFO @ Sun, 02 Jun 2019 22:07:13: #2 predicted fragment length is 2 bps INFO @ Sun, 02 Jun 2019 22:07:13: #2 alternative fragment length(s) may be 2,15,37,489,515,538,574 bps INFO @ Sun, 02 Jun 2019 22:07:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529209/SRX529209.05_model.r WARNING @ Sun, 02 Jun 2019 22:07:13: #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, 02 Jun 2019 22:07:13: #2 You may need to consider one of the other alternative d(s): 2,15,37,489,515,538,574 WARNING @ Sun, 02 Jun 2019 22:07:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 22:07:13: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:07:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:07:19: 16000000 INFO @ Sun, 02 Jun 2019 22:07:28: 17000000 INFO @ Sun, 02 Jun 2019 22:07:30: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 22:07:30: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 22:07:30: #1 total tags in treatment: 17223604 INFO @ Sun, 02 Jun 2019 22:07:30: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:07:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 22:07:31: #1 tags after filtering in treatment: 17223604 INFO @ Sun, 02 Jun 2019 22:07:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:07:31: #1 finished! INFO @ Sun, 02 Jun 2019 22:07:31: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:07:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:07:32: #2 number of paired peaks: 209 WARNING @ Sun, 02 Jun 2019 22:07:32: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Sun, 02 Jun 2019 22:07:32: start model_add_line... INFO @ Sun, 02 Jun 2019 22:07:32: start X-correlation... INFO @ Sun, 02 Jun 2019 22:07:32: end of X-cor INFO @ Sun, 02 Jun 2019 22:07:32: #2 finished! INFO @ Sun, 02 Jun 2019 22:07:32: #2 predicted fragment length is 2 bps INFO @ Sun, 02 Jun 2019 22:07:32: #2 alternative fragment length(s) may be 2,15,37,489,515,538,574 bps INFO @ Sun, 02 Jun 2019 22:07:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529209/SRX529209.10_model.r WARNING @ Sun, 02 Jun 2019 22:07:32: #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, 02 Jun 2019 22:07:32: #2 You may need to consider one of the other alternative d(s): 2,15,37,489,515,538,574 WARNING @ Sun, 02 Jun 2019 22:07:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 22:07:32: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:07:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:07:48: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:07:51: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:08:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529209/SRX529209.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:08:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529209/SRX529209.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:08:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529209/SRX529209.20_summits.bed INFO @ Sun, 02 Jun 2019 22:08:06: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:08:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529209/SRX529209.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:08:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529209/SRX529209.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:08:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529209/SRX529209.05_summits.bed INFO @ Sun, 02 Jun 2019 22:08:08: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:08:10: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:08:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529209/SRX529209.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:08:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529209/SRX529209.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:08:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529209/SRX529209.10_summits.bed INFO @ Sun, 02 Jun 2019 22:08:28: Done! pass1 - making usageList (0 chroms): 1 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。