Job ID = 2589895 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,936,104 reads read : 5,936,104 reads written : 5,936,104 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947536.sra.cache’: 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: 00:01:00 5936104 reads; of these: 5936104 (100.00%) were unpaired; of these: 80701 (1.36%) aligned 0 times 4969759 (83.72%) aligned exactly 1 time 885644 (14.92%) aligned >1 times 98.64% overall alignment rate Time searching: 00:01:00 Overall time: 00:01:00 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] 644994 / 5855403 = 0.1102 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 18:44:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331299/SRX331299.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331299/SRX331299.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331299/SRX331299.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331299/SRX331299.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 18:44:30: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:44:30: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:44:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331299/SRX331299.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331299/SRX331299.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331299/SRX331299.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331299/SRX331299.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 18:44:31: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:44:31: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:44:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331299/SRX331299.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331299/SRX331299.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331299/SRX331299.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331299/SRX331299.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 18:44:32: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:44:32: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:44:37: 1000000 INFO @ Mon, 12 Aug 2019 18:44:39: 1000000 INFO @ Mon, 12 Aug 2019 18:44:40: 1000000 INFO @ Mon, 12 Aug 2019 18:44:45: 2000000 INFO @ Mon, 12 Aug 2019 18:44:46: 2000000 INFO @ Mon, 12 Aug 2019 18:44:49: 2000000 INFO @ Mon, 12 Aug 2019 18:44:52: 3000000 INFO @ Mon, 12 Aug 2019 18:44:53: 3000000 INFO @ Mon, 12 Aug 2019 18:44:57: 3000000 INFO @ Mon, 12 Aug 2019 18:44:59: 4000000 INFO @ Mon, 12 Aug 2019 18:45:00: 4000000 INFO @ Mon, 12 Aug 2019 18:45:05: 4000000 INFO @ Mon, 12 Aug 2019 18:45:07: 5000000 INFO @ Mon, 12 Aug 2019 18:45:08: 5000000 INFO @ Mon, 12 Aug 2019 18:45:08: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:45:08: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:45:08: #1 total tags in treatment: 5210409 INFO @ Mon, 12 Aug 2019 18:45:08: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:45:08: #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 18:45:08: #1 tags after filtering in treatment: 5210409 INFO @ Mon, 12 Aug 2019 18:45:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:45:08: #1 finished! INFO @ Mon, 12 Aug 2019 18:45:08: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:45:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:45:09: #2 number of paired peaks: 375 WARNING @ Mon, 12 Aug 2019 18:45:09: Fewer paired peaks (375) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 375 pairs to build model! INFO @ Mon, 12 Aug 2019 18:45:09: start model_add_line... INFO @ Mon, 12 Aug 2019 18:45:09: start X-correlation... INFO @ Mon, 12 Aug 2019 18:45:09: end of X-cor INFO @ Mon, 12 Aug 2019 18:45:09: #2 finished! INFO @ Mon, 12 Aug 2019 18:45:09: #2 predicted fragment length is 34 bps INFO @ Mon, 12 Aug 2019 18:45:09: #2 alternative fragment length(s) may be 3,34 bps INFO @ Mon, 12 Aug 2019 18:45:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331299/SRX331299.05_model.r WARNING @ Mon, 12 Aug 2019 18:45:09: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:45:09: #2 You may need to consider one of the other alternative d(s): 3,34 WARNING @ Mon, 12 Aug 2019 18:45:09: #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 18:45:09: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:45:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:45:09: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:45:09: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:45:09: #1 total tags in treatment: 5210409 INFO @ Mon, 12 Aug 2019 18:45:09: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:45:09: #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 18:45:09: #1 tags after filtering in treatment: 5210409 INFO @ Mon, 12 Aug 2019 18:45:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:45:09: #1 finished! INFO @ Mon, 12 Aug 2019 18:45:09: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:45:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:45:10: #2 number of paired peaks: 375 WARNING @ Mon, 12 Aug 2019 18:45:10: Fewer paired peaks (375) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 375 pairs to build model! INFO @ Mon, 12 Aug 2019 18:45:10: start model_add_line... INFO @ Mon, 12 Aug 2019 18:45:10: start X-correlation... INFO @ Mon, 12 Aug 2019 18:45:10: end of X-cor INFO @ Mon, 12 Aug 2019 18:45:10: #2 finished! INFO @ Mon, 12 Aug 2019 18:45:10: #2 predicted fragment length is 34 bps INFO @ Mon, 12 Aug 2019 18:45:10: #2 alternative fragment length(s) may be 3,34 bps INFO @ Mon, 12 Aug 2019 18:45:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331299/SRX331299.10_model.r WARNING @ Mon, 12 Aug 2019 18:45:10: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:45:10: #2 You may need to consider one of the other alternative d(s): 3,34 WARNING @ Mon, 12 Aug 2019 18:45:10: #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 18:45:10: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:45:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:45:13: 5000000 INFO @ Mon, 12 Aug 2019 18:45:15: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:45:15: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:45:15: #1 total tags in treatment: 5210409 INFO @ Mon, 12 Aug 2019 18:45:15: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:45:15: #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 18:45:15: #1 tags after filtering in treatment: 5210409 INFO @ Mon, 12 Aug 2019 18:45:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:45:15: #1 finished! INFO @ Mon, 12 Aug 2019 18:45:15: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:45:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:45:15: #2 number of paired peaks: 375 WARNING @ Mon, 12 Aug 2019 18:45:15: Fewer paired peaks (375) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 375 pairs to build model! INFO @ Mon, 12 Aug 2019 18:45:15: start model_add_line... INFO @ Mon, 12 Aug 2019 18:45:15: start X-correlation... INFO @ Mon, 12 Aug 2019 18:45:15: end of X-cor INFO @ Mon, 12 Aug 2019 18:45:15: #2 finished! INFO @ Mon, 12 Aug 2019 18:45:15: #2 predicted fragment length is 34 bps INFO @ Mon, 12 Aug 2019 18:45:15: #2 alternative fragment length(s) may be 3,34 bps INFO @ Mon, 12 Aug 2019 18:45:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331299/SRX331299.20_model.r WARNING @ Mon, 12 Aug 2019 18:45:15: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:45:15: #2 You may need to consider one of the other alternative d(s): 3,34 WARNING @ Mon, 12 Aug 2019 18:45:15: #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 18:45:15: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:45:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:45:24: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:45:25: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:45:31: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:45:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331299/SRX331299.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:45:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331299/SRX331299.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:45:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331299/SRX331299.05_summits.bed INFO @ Mon, 12 Aug 2019 18:45:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (401 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:45:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331299/SRX331299.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:45:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331299/SRX331299.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:45:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331299/SRX331299.10_summits.bed INFO @ Mon, 12 Aug 2019 18:45:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (172 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:45:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331299/SRX331299.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:45:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331299/SRX331299.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:45:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331299/SRX331299.20_summits.bed INFO @ Mon, 12 Aug 2019 18:45:38: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (60 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。