Job ID = 2589358 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,518,687 reads read : 22,518,687 reads written : 22,518,687 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: 00:05:25 22518687 reads; of these: 22518687 (100.00%) were unpaired; of these: 1420933 (6.31%) aligned 0 times 17302368 (76.84%) aligned exactly 1 time 3795386 (16.85%) aligned >1 times 93.69% overall alignment rate Time searching: 00:05:25 Overall time: 00:05:25 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] 12449664 / 21097754 = 0.5901 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 17:53:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078711/SRX1078711.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078711/SRX1078711.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078711/SRX1078711.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078711/SRX1078711.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 17:53:14: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:53:14: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:53:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078711/SRX1078711.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078711/SRX1078711.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078711/SRX1078711.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078711/SRX1078711.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 17:53:15: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:53:15: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:53:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078711/SRX1078711.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078711/SRX1078711.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078711/SRX1078711.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078711/SRX1078711.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 17:53:16: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:53:16: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:53:21: 1000000 INFO @ Mon, 12 Aug 2019 17:53:22: 1000000 INFO @ Mon, 12 Aug 2019 17:53:23: 1000000 INFO @ Mon, 12 Aug 2019 17:53:29: 2000000 INFO @ Mon, 12 Aug 2019 17:53:30: 2000000 INFO @ Mon, 12 Aug 2019 17:53:30: 2000000 INFO @ Mon, 12 Aug 2019 17:53:36: 3000000 INFO @ Mon, 12 Aug 2019 17:53:37: 3000000 INFO @ Mon, 12 Aug 2019 17:53:37: 3000000 INFO @ Mon, 12 Aug 2019 17:53:43: 4000000 INFO @ Mon, 12 Aug 2019 17:53:43: 4000000 INFO @ Mon, 12 Aug 2019 17:53:44: 4000000 INFO @ Mon, 12 Aug 2019 17:53:50: 5000000 INFO @ Mon, 12 Aug 2019 17:53:50: 5000000 INFO @ Mon, 12 Aug 2019 17:53:51: 5000000 INFO @ Mon, 12 Aug 2019 17:53:57: 6000000 INFO @ Mon, 12 Aug 2019 17:53:57: 6000000 INFO @ Mon, 12 Aug 2019 17:53:58: 6000000 INFO @ Mon, 12 Aug 2019 17:54:03: 7000000 INFO @ Mon, 12 Aug 2019 17:54:04: 7000000 INFO @ Mon, 12 Aug 2019 17:54:05: 7000000 INFO @ Mon, 12 Aug 2019 17:54:10: 8000000 INFO @ Mon, 12 Aug 2019 17:54:12: 8000000 INFO @ Mon, 12 Aug 2019 17:54:12: 8000000 INFO @ Mon, 12 Aug 2019 17:54:14: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 17:54:14: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 17:54:14: #1 total tags in treatment: 8648090 INFO @ Mon, 12 Aug 2019 17:54:14: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:54:14: #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 17:54:15: #1 tags after filtering in treatment: 8648090 INFO @ Mon, 12 Aug 2019 17:54:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:54:15: #1 finished! INFO @ Mon, 12 Aug 2019 17:54:15: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:54:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:54:15: #2 number of paired peaks: 690 WARNING @ Mon, 12 Aug 2019 17:54:15: Fewer paired peaks (690) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 690 pairs to build model! INFO @ Mon, 12 Aug 2019 17:54:15: start model_add_line... INFO @ Mon, 12 Aug 2019 17:54:16: start X-correlation... INFO @ Mon, 12 Aug 2019 17:54:16: end of X-cor INFO @ Mon, 12 Aug 2019 17:54:16: #2 finished! INFO @ Mon, 12 Aug 2019 17:54:16: #2 predicted fragment length is 60 bps INFO @ Mon, 12 Aug 2019 17:54:16: #2 alternative fragment length(s) may be 4,60 bps INFO @ Mon, 12 Aug 2019 17:54:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078711/SRX1078711.20_model.r WARNING @ Mon, 12 Aug 2019 17:54:16: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:54:16: #2 You may need to consider one of the other alternative d(s): 4,60 WARNING @ Mon, 12 Aug 2019 17:54:16: #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 17:54:16: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:54:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:54:16: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 17:54:16: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 17:54:16: #1 total tags in treatment: 8648090 INFO @ Mon, 12 Aug 2019 17:54:16: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:54:16: #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 17:54:16: #1 tags after filtering in treatment: 8648090 INFO @ Mon, 12 Aug 2019 17:54:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:54:16: #1 finished! INFO @ Mon, 12 Aug 2019 17:54:16: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:54:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:54:17: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 17:54:17: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 17:54:17: #1 total tags in treatment: 8648090 INFO @ Mon, 12 Aug 2019 17:54:17: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:54:17: #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 17:54:17: #1 tags after filtering in treatment: 8648090 INFO @ Mon, 12 Aug 2019 17:54:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:54:17: #1 finished! INFO @ Mon, 12 Aug 2019 17:54:17: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:54:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:54:17: #2 number of paired peaks: 690 WARNING @ Mon, 12 Aug 2019 17:54:17: Fewer paired peaks (690) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 690 pairs to build model! INFO @ Mon, 12 Aug 2019 17:54:17: start model_add_line... INFO @ Mon, 12 Aug 2019 17:54:17: start X-correlation... INFO @ Mon, 12 Aug 2019 17:54:17: end of X-cor INFO @ Mon, 12 Aug 2019 17:54:17: #2 finished! INFO @ Mon, 12 Aug 2019 17:54:17: #2 predicted fragment length is 60 bps INFO @ Mon, 12 Aug 2019 17:54:17: #2 alternative fragment length(s) may be 4,60 bps INFO @ Mon, 12 Aug 2019 17:54:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078711/SRX1078711.05_model.r WARNING @ Mon, 12 Aug 2019 17:54:17: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:54:17: #2 You may need to consider one of the other alternative d(s): 4,60 WARNING @ Mon, 12 Aug 2019 17:54:17: #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 17:54:17: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:54:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:54:18: #2 number of paired peaks: 690 WARNING @ Mon, 12 Aug 2019 17:54:18: Fewer paired peaks (690) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 690 pairs to build model! INFO @ Mon, 12 Aug 2019 17:54:18: start model_add_line... INFO @ Mon, 12 Aug 2019 17:54:18: start X-correlation... INFO @ Mon, 12 Aug 2019 17:54:18: end of X-cor INFO @ Mon, 12 Aug 2019 17:54:18: #2 finished! INFO @ Mon, 12 Aug 2019 17:54:18: #2 predicted fragment length is 60 bps INFO @ Mon, 12 Aug 2019 17:54:18: #2 alternative fragment length(s) may be 4,60 bps INFO @ Mon, 12 Aug 2019 17:54:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078711/SRX1078711.10_model.r WARNING @ Mon, 12 Aug 2019 17:54:18: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:54:18: #2 You may need to consider one of the other alternative d(s): 4,60 WARNING @ Mon, 12 Aug 2019 17:54:18: #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 17:54:18: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:54:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:54:40: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:54:41: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:54:42: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:54:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1078711/SRX1078711.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:54:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1078711/SRX1078711.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:54:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1078711/SRX1078711.20_summits.bed INFO @ Mon, 12 Aug 2019 17:54:51: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (366 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:54:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1078711/SRX1078711.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:54:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1078711/SRX1078711.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:54:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1078711/SRX1078711.05_summits.bed INFO @ Mon, 12 Aug 2019 17:54:53: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1711 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:54:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1078711/SRX1078711.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:54:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1078711/SRX1078711.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:54:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1078711/SRX1078711.10_summits.bed INFO @ Mon, 12 Aug 2019 17:54:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (859 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。