Job ID = 1293133 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,297,646 reads read : 24,297,646 reads written : 24,297,646 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: 00:05:33 24297646 reads; of these: 24297646 (100.00%) were unpaired; of these: 1569649 (6.46%) aligned 0 times 19710653 (81.12%) aligned exactly 1 time 3017344 (12.42%) aligned >1 times 93.54% overall alignment rate Time searching: 00:05:33 Overall time: 00:05:33 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] 3368701 / 22727997 = 0.1482 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 22:19:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402706/SRX5402706.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402706/SRX5402706.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402706/SRX5402706.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402706/SRX5402706.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 22:19:45: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:19:45: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:19:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402706/SRX5402706.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402706/SRX5402706.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402706/SRX5402706.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402706/SRX5402706.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 22:19:45: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:19:45: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:19:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402706/SRX5402706.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402706/SRX5402706.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402706/SRX5402706.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402706/SRX5402706.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 22:19:45: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:19:45: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:19:53: 1000000 INFO @ Sun, 02 Jun 2019 22:19:53: 1000000 INFO @ Sun, 02 Jun 2019 22:19:55: 1000000 INFO @ Sun, 02 Jun 2019 22:20:01: 2000000 INFO @ Sun, 02 Jun 2019 22:20:01: 2000000 INFO @ Sun, 02 Jun 2019 22:20:05: 2000000 INFO @ Sun, 02 Jun 2019 22:20:08: 3000000 INFO @ Sun, 02 Jun 2019 22:20:09: 3000000 INFO @ Sun, 02 Jun 2019 22:20:14: 3000000 INFO @ Sun, 02 Jun 2019 22:20:16: 4000000 INFO @ Sun, 02 Jun 2019 22:20:16: 4000000 INFO @ Sun, 02 Jun 2019 22:20:24: 5000000 INFO @ Sun, 02 Jun 2019 22:20:24: 4000000 INFO @ Sun, 02 Jun 2019 22:20:24: 5000000 INFO @ Sun, 02 Jun 2019 22:20:31: 6000000 INFO @ Sun, 02 Jun 2019 22:20:32: 6000000 INFO @ Sun, 02 Jun 2019 22:20:33: 5000000 INFO @ Sun, 02 Jun 2019 22:20:39: 7000000 INFO @ Sun, 02 Jun 2019 22:20:40: 7000000 INFO @ Sun, 02 Jun 2019 22:20:43: 6000000 INFO @ Sun, 02 Jun 2019 22:20:47: 8000000 INFO @ Sun, 02 Jun 2019 22:20:47: 8000000 INFO @ Sun, 02 Jun 2019 22:20:53: 7000000 INFO @ Sun, 02 Jun 2019 22:20:55: 9000000 INFO @ Sun, 02 Jun 2019 22:20:55: 9000000 INFO @ Sun, 02 Jun 2019 22:21:02: 8000000 INFO @ Sun, 02 Jun 2019 22:21:03: 10000000 INFO @ Sun, 02 Jun 2019 22:21:03: 10000000 INFO @ Sun, 02 Jun 2019 22:21:10: 11000000 INFO @ Sun, 02 Jun 2019 22:21:10: 11000000 INFO @ Sun, 02 Jun 2019 22:21:12: 9000000 INFO @ Sun, 02 Jun 2019 22:21:18: 12000000 INFO @ Sun, 02 Jun 2019 22:21:18: 12000000 INFO @ Sun, 02 Jun 2019 22:21:21: 10000000 INFO @ Sun, 02 Jun 2019 22:21:26: 13000000 INFO @ Sun, 02 Jun 2019 22:21:26: 13000000 INFO @ Sun, 02 Jun 2019 22:21:31: 11000000 INFO @ Sun, 02 Jun 2019 22:21:34: 14000000 INFO @ Sun, 02 Jun 2019 22:21:34: 14000000 INFO @ Sun, 02 Jun 2019 22:21:41: 12000000 INFO @ Sun, 02 Jun 2019 22:21:41: 15000000 INFO @ Sun, 02 Jun 2019 22:21:41: 15000000 INFO @ Sun, 02 Jun 2019 22:21:49: 16000000 INFO @ Sun, 02 Jun 2019 22:21:49: 16000000 INFO @ Sun, 02 Jun 2019 22:21:51: 13000000 INFO @ Sun, 02 Jun 2019 22:21:57: 17000000 INFO @ Sun, 02 Jun 2019 22:21:57: 17000000 INFO @ Sun, 02 Jun 2019 22:22:00: 14000000 INFO @ Sun, 02 Jun 2019 22:22:04: 18000000 INFO @ Sun, 02 Jun 2019 22:22:05: 18000000 INFO @ Sun, 02 Jun 2019 22:22:10: 15000000 INFO @ Sun, 02 Jun 2019 22:22:12: 19000000 INFO @ Sun, 02 Jun 2019 22:22:12: 19000000 INFO @ Sun, 02 Jun 2019 22:22:15: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:22:15: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:22:15: #1 total tags in treatment: 19359296 INFO @ Sun, 02 Jun 2019 22:22:15: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:22:15: #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 22:22:15: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:22:15: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:22:15: #1 total tags in treatment: 19359296 INFO @ Sun, 02 Jun 2019 22:22:15: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:22:15: #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 22:22:15: #1 tags after filtering in treatment: 19359296 INFO @ Sun, 02 Jun 2019 22:22:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:22:15: #1 finished! INFO @ Sun, 02 Jun 2019 22:22:15: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:22:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:22:16: #1 tags after filtering in treatment: 19359296 INFO @ Sun, 02 Jun 2019 22:22:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:22:16: #1 finished! INFO @ Sun, 02 Jun 2019 22:22:16: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:22:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:22:17: #2 number of paired peaks: 129 WARNING @ Sun, 02 Jun 2019 22:22:17: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Sun, 02 Jun 2019 22:22:17: start model_add_line... INFO @ Sun, 02 Jun 2019 22:22:17: start X-correlation... INFO @ Sun, 02 Jun 2019 22:22:17: end of X-cor INFO @ Sun, 02 Jun 2019 22:22:17: #2 finished! INFO @ Sun, 02 Jun 2019 22:22:17: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:22:17: #2 alternative fragment length(s) may be 1,45,523 bps INFO @ Sun, 02 Jun 2019 22:22:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402706/SRX5402706.10_model.r WARNING @ Sun, 02 Jun 2019 22:22:17: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:22:17: #2 You may need to consider one of the other alternative d(s): 1,45,523 WARNING @ Sun, 02 Jun 2019 22:22:17: #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 22:22:17: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:22:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:22:17: #2 number of paired peaks: 129 WARNING @ Sun, 02 Jun 2019 22:22:17: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Sun, 02 Jun 2019 22:22:17: start model_add_line... INFO @ Sun, 02 Jun 2019 22:22:17: start X-correlation... INFO @ Sun, 02 Jun 2019 22:22:17: end of X-cor INFO @ Sun, 02 Jun 2019 22:22:17: #2 finished! INFO @ Sun, 02 Jun 2019 22:22:17: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:22:17: #2 alternative fragment length(s) may be 1,45,523 bps INFO @ Sun, 02 Jun 2019 22:22:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402706/SRX5402706.20_model.r WARNING @ Sun, 02 Jun 2019 22:22:17: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:22:17: #2 You may need to consider one of the other alternative d(s): 1,45,523 WARNING @ Sun, 02 Jun 2019 22:22:17: #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 22:22:17: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:22:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:22:19: 16000000 INFO @ Sun, 02 Jun 2019 22:22:29: 17000000 INFO @ Sun, 02 Jun 2019 22:22:38: 18000000 INFO @ Sun, 02 Jun 2019 22:22:48: 19000000 INFO @ Sun, 02 Jun 2019 22:22:51: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:22:51: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:22:51: #1 total tags in treatment: 19359296 INFO @ Sun, 02 Jun 2019 22:22:51: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:22:51: #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 22:22:51: #1 tags after filtering in treatment: 19359296 INFO @ Sun, 02 Jun 2019 22:22:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:22:51: #1 finished! INFO @ Sun, 02 Jun 2019 22:22:51: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:22:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:22:53: #2 number of paired peaks: 129 WARNING @ Sun, 02 Jun 2019 22:22:53: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Sun, 02 Jun 2019 22:22:53: start model_add_line... INFO @ Sun, 02 Jun 2019 22:22:53: start X-correlation... INFO @ Sun, 02 Jun 2019 22:22:53: end of X-cor INFO @ Sun, 02 Jun 2019 22:22:53: #2 finished! INFO @ Sun, 02 Jun 2019 22:22:53: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:22:53: #2 alternative fragment length(s) may be 1,45,523 bps INFO @ Sun, 02 Jun 2019 22:22:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402706/SRX5402706.05_model.r WARNING @ Sun, 02 Jun 2019 22:22:53: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:22:53: #2 You may need to consider one of the other alternative d(s): 1,45,523 WARNING @ Sun, 02 Jun 2019 22:22:53: #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 22:22:53: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:22:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:22:59: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:22:59: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:23:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402706/SRX5402706.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:23:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402706/SRX5402706.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:23:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402706/SRX5402706.20_summits.bed INFO @ Sun, 02 Jun 2019 22:23:18: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:23:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402706/SRX5402706.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:23:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402706/SRX5402706.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:23:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402706/SRX5402706.10_summits.bed INFO @ Sun, 02 Jun 2019 22:23:18: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:23:35: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:23:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402706/SRX5402706.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:23:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402706/SRX5402706.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:23:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402706/SRX5402706.05_summits.bed INFO @ Sun, 02 Jun 2019 22:23:54: 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。