Job ID = 1290591 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 26,510,838 reads read : 26,510,838 reads written : 26,510,838 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: 00:03:49 26510838 reads; of these: 26510838 (100.00%) were unpaired; of these: 19345310 (72.97%) aligned 0 times 5867761 (22.13%) aligned exactly 1 time 1297767 (4.90%) aligned >1 times 27.03% overall alignment rate Time searching: 00:03:49 Overall time: 00:03:49 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_rmdupse_core] 619467 / 7165528 = 0.0865 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 @ Sat, 01 Jun 2019 21:51:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX373272/SRX373272.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX373272/SRX373272.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX373272/SRX373272.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX373272/SRX373272.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 @ Sat, 01 Jun 2019 21:51:31: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:51:31: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:51:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX373272/SRX373272.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX373272/SRX373272.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX373272/SRX373272.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX373272/SRX373272.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 @ Sat, 01 Jun 2019 21:51:31: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:51:31: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:51:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX373272/SRX373272.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX373272/SRX373272.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX373272/SRX373272.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX373272/SRX373272.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 @ Sat, 01 Jun 2019 21:51:31: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:51:31: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:51:40: 1000000 INFO @ Sat, 01 Jun 2019 21:51:40: 1000000 INFO @ Sat, 01 Jun 2019 21:51:43: 1000000 INFO @ Sat, 01 Jun 2019 21:51:49: 2000000 INFO @ Sat, 01 Jun 2019 21:51:49: 2000000 INFO @ Sat, 01 Jun 2019 21:51:54: 2000000 INFO @ Sat, 01 Jun 2019 21:51:58: 3000000 INFO @ Sat, 01 Jun 2019 21:51:58: 3000000 INFO @ Sat, 01 Jun 2019 21:52:05: 3000000 INFO @ Sat, 01 Jun 2019 21:52:06: 4000000 INFO @ Sat, 01 Jun 2019 21:52:07: 4000000 INFO @ Sat, 01 Jun 2019 21:52:15: 5000000 INFO @ Sat, 01 Jun 2019 21:52:16: 4000000 INFO @ Sat, 01 Jun 2019 21:52:16: 5000000 INFO @ Sat, 01 Jun 2019 21:52:24: 6000000 INFO @ Sat, 01 Jun 2019 21:52:25: 6000000 INFO @ Sat, 01 Jun 2019 21:52:28: 5000000 INFO @ Sat, 01 Jun 2019 21:52:29: #1 tag size is determined as 51 bps INFO @ Sat, 01 Jun 2019 21:52:29: #1 tag size = 51 INFO @ Sat, 01 Jun 2019 21:52:29: #1 total tags in treatment: 6546061 INFO @ Sat, 01 Jun 2019 21:52:29: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:52:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:52:29: #1 tags after filtering in treatment: 6546061 INFO @ Sat, 01 Jun 2019 21:52:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:52:29: #1 finished! INFO @ Sat, 01 Jun 2019 21:52:29: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:52:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:52:30: #2 number of paired peaks: 371 WARNING @ Sat, 01 Jun 2019 21:52:30: Fewer paired peaks (371) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 371 pairs to build model! INFO @ Sat, 01 Jun 2019 21:52:30: start model_add_line... INFO @ Sat, 01 Jun 2019 21:52:30: start X-correlation... INFO @ Sat, 01 Jun 2019 21:52:30: end of X-cor INFO @ Sat, 01 Jun 2019 21:52:30: #2 finished! INFO @ Sat, 01 Jun 2019 21:52:30: #2 predicted fragment length is 49 bps INFO @ Sat, 01 Jun 2019 21:52:30: #2 alternative fragment length(s) may be 4,49,514,567 bps INFO @ Sat, 01 Jun 2019 21:52:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX373272/SRX373272.10_model.r WARNING @ Sat, 01 Jun 2019 21:52:30: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 01 Jun 2019 21:52:30: #2 You may need to consider one of the other alternative d(s): 4,49,514,567 WARNING @ Sat, 01 Jun 2019 21:52:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 01 Jun 2019 21:52:30: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:52:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:52:30: #1 tag size is determined as 51 bps INFO @ Sat, 01 Jun 2019 21:52:30: #1 tag size = 51 INFO @ Sat, 01 Jun 2019 21:52:30: #1 total tags in treatment: 6546061 INFO @ Sat, 01 Jun 2019 21:52:30: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:52:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:52:31: #1 tags after filtering in treatment: 6546061 INFO @ Sat, 01 Jun 2019 21:52:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:52:31: #1 finished! INFO @ Sat, 01 Jun 2019 21:52:31: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:52:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:52:31: #2 number of paired peaks: 371 WARNING @ Sat, 01 Jun 2019 21:52:31: Fewer paired peaks (371) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 371 pairs to build model! INFO @ Sat, 01 Jun 2019 21:52:31: start model_add_line... INFO @ Sat, 01 Jun 2019 21:52:31: start X-correlation... INFO @ Sat, 01 Jun 2019 21:52:31: end of X-cor INFO @ Sat, 01 Jun 2019 21:52:31: #2 finished! INFO @ Sat, 01 Jun 2019 21:52:31: #2 predicted fragment length is 49 bps INFO @ Sat, 01 Jun 2019 21:52:31: #2 alternative fragment length(s) may be 4,49,514,567 bps INFO @ Sat, 01 Jun 2019 21:52:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX373272/SRX373272.20_model.r WARNING @ Sat, 01 Jun 2019 21:52:31: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 01 Jun 2019 21:52:31: #2 You may need to consider one of the other alternative d(s): 4,49,514,567 WARNING @ Sat, 01 Jun 2019 21:52:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 01 Jun 2019 21:52:31: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:52:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:52:40: 6000000 INFO @ Sat, 01 Jun 2019 21:52:46: #1 tag size is determined as 51 bps INFO @ Sat, 01 Jun 2019 21:52:46: #1 tag size = 51 INFO @ Sat, 01 Jun 2019 21:52:46: #1 total tags in treatment: 6546061 INFO @ Sat, 01 Jun 2019 21:52:46: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:52:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:52:47: #1 tags after filtering in treatment: 6546061 INFO @ Sat, 01 Jun 2019 21:52:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:52:47: #1 finished! INFO @ Sat, 01 Jun 2019 21:52:47: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:52:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:52:47: #2 number of paired peaks: 371 WARNING @ Sat, 01 Jun 2019 21:52:47: Fewer paired peaks (371) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 371 pairs to build model! INFO @ Sat, 01 Jun 2019 21:52:47: start model_add_line... INFO @ Sat, 01 Jun 2019 21:52:47: start X-correlation... INFO @ Sat, 01 Jun 2019 21:52:47: end of X-cor INFO @ Sat, 01 Jun 2019 21:52:47: #2 finished! INFO @ Sat, 01 Jun 2019 21:52:47: #2 predicted fragment length is 49 bps INFO @ Sat, 01 Jun 2019 21:52:47: #2 alternative fragment length(s) may be 4,49,514,567 bps INFO @ Sat, 01 Jun 2019 21:52:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX373272/SRX373272.05_model.r WARNING @ Sat, 01 Jun 2019 21:52:47: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 01 Jun 2019 21:52:47: #2 You may need to consider one of the other alternative d(s): 4,49,514,567 WARNING @ Sat, 01 Jun 2019 21:52:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 01 Jun 2019 21:52:47: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:52:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:52:50: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:52:52: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:53:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX373272/SRX373272.10_peaks.xls INFO @ Sat, 01 Jun 2019 21:53:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX373272/SRX373272.10_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:53:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX373272/SRX373272.10_summits.bed INFO @ Sat, 01 Jun 2019 21:53:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (343 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 21:53:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX373272/SRX373272.20_peaks.xls INFO @ Sat, 01 Jun 2019 21:53:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX373272/SRX373272.20_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:53:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX373272/SRX373272.20_summits.bed INFO @ Sat, 01 Jun 2019 21:53:02: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (125 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 21:53:07: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:53:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX373272/SRX373272.05_peaks.xls INFO @ Sat, 01 Jun 2019 21:53:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX373272/SRX373272.05_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:53:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX373272/SRX373272.05_summits.bed INFO @ Sat, 01 Jun 2019 21:53:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (585 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。