Job ID = 2589624 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,756,008 reads read : 5,756,008 reads written : 5,756,008 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: 00:00:50 5756008 reads; of these: 5756008 (100.00%) were unpaired; of these: 1468556 (25.51%) aligned 0 times 3635434 (63.16%) aligned exactly 1 time 652018 (11.33%) aligned >1 times 74.49% overall alignment rate Time searching: 00:00:50 Overall time: 00:00:50 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] 312335 / 4287452 = 0.0728 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 18:08:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX277063/SRX277063.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX277063/SRX277063.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX277063/SRX277063.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX277063/SRX277063.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 18:08:32: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:08:32: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:08:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX277063/SRX277063.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX277063/SRX277063.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX277063/SRX277063.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX277063/SRX277063.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 18:08:33: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:08:33: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:08:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX277063/SRX277063.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX277063/SRX277063.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX277063/SRX277063.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX277063/SRX277063.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 18:08:34: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:08:34: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:08:41: 1000000 INFO @ Mon, 12 Aug 2019 18:08:42: 1000000 INFO @ Mon, 12 Aug 2019 18:08:42: 1000000 INFO @ Mon, 12 Aug 2019 18:08:49: 2000000 INFO @ Mon, 12 Aug 2019 18:08:50: 2000000 INFO @ Mon, 12 Aug 2019 18:08:51: 2000000 INFO @ Mon, 12 Aug 2019 18:08:56: 3000000 INFO @ Mon, 12 Aug 2019 18:08:59: 3000000 INFO @ Mon, 12 Aug 2019 18:09:01: 3000000 INFO @ Mon, 12 Aug 2019 18:09:02: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:09:02: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:09:02: #1 total tags in treatment: 3975117 INFO @ Mon, 12 Aug 2019 18:09:02: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:09:02: #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 18:09:02: #1 tags after filtering in treatment: 3975117 INFO @ Mon, 12 Aug 2019 18:09:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:09:02: #1 finished! INFO @ Mon, 12 Aug 2019 18:09:02: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:09:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:09:03: #2 number of paired peaks: 495 WARNING @ Mon, 12 Aug 2019 18:09:03: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Mon, 12 Aug 2019 18:09:03: start model_add_line... INFO @ Mon, 12 Aug 2019 18:09:03: start X-correlation... INFO @ Mon, 12 Aug 2019 18:09:03: end of X-cor INFO @ Mon, 12 Aug 2019 18:09:03: #2 finished! INFO @ Mon, 12 Aug 2019 18:09:03: #2 predicted fragment length is 38 bps INFO @ Mon, 12 Aug 2019 18:09:03: #2 alternative fragment length(s) may be 4,38,71,102,561 bps INFO @ Mon, 12 Aug 2019 18:09:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX277063/SRX277063.20_model.r WARNING @ Mon, 12 Aug 2019 18:09:03: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:09:03: #2 You may need to consider one of the other alternative d(s): 4,38,71,102,561 WARNING @ Mon, 12 Aug 2019 18:09:03: #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 18:09:03: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:09:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:09:08: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:09:08: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:09:08: #1 total tags in treatment: 3975117 INFO @ Mon, 12 Aug 2019 18:09:08: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:09:08: #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 18:09:08: #1 tags after filtering in treatment: 3975117 INFO @ Mon, 12 Aug 2019 18:09:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:09:08: #1 finished! INFO @ Mon, 12 Aug 2019 18:09:08: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:09:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:09:08: #2 number of paired peaks: 495 WARNING @ Mon, 12 Aug 2019 18:09:08: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Mon, 12 Aug 2019 18:09:08: start model_add_line... INFO @ Mon, 12 Aug 2019 18:09:08: start X-correlation... INFO @ Mon, 12 Aug 2019 18:09:08: end of X-cor INFO @ Mon, 12 Aug 2019 18:09:08: #2 finished! INFO @ Mon, 12 Aug 2019 18:09:08: #2 predicted fragment length is 38 bps INFO @ Mon, 12 Aug 2019 18:09:08: #2 alternative fragment length(s) may be 4,38,71,102,561 bps INFO @ Mon, 12 Aug 2019 18:09:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX277063/SRX277063.05_model.r WARNING @ Mon, 12 Aug 2019 18:09:08: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:09:08: #2 You may need to consider one of the other alternative d(s): 4,38,71,102,561 WARNING @ Mon, 12 Aug 2019 18:09:08: #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 18:09:08: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:09:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:09:09: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:09:09: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:09:09: #1 total tags in treatment: 3975117 INFO @ Mon, 12 Aug 2019 18:09:09: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:09:09: #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 18:09:09: #1 tags after filtering in treatment: 3975117 INFO @ Mon, 12 Aug 2019 18:09:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:09:09: #1 finished! INFO @ Mon, 12 Aug 2019 18:09:09: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:09:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:09:09: #2 number of paired peaks: 495 WARNING @ Mon, 12 Aug 2019 18:09:09: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Mon, 12 Aug 2019 18:09:09: start model_add_line... INFO @ Mon, 12 Aug 2019 18:09:10: start X-correlation... INFO @ Mon, 12 Aug 2019 18:09:10: end of X-cor INFO @ Mon, 12 Aug 2019 18:09:10: #2 finished! INFO @ Mon, 12 Aug 2019 18:09:10: #2 predicted fragment length is 38 bps INFO @ Mon, 12 Aug 2019 18:09:10: #2 alternative fragment length(s) may be 4,38,71,102,561 bps INFO @ Mon, 12 Aug 2019 18:09:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX277063/SRX277063.10_model.r WARNING @ Mon, 12 Aug 2019 18:09:10: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:09:10: #2 You may need to consider one of the other alternative d(s): 4,38,71,102,561 WARNING @ Mon, 12 Aug 2019 18:09:10: #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 18:09:10: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:09:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:09:15: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:09:20: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:09:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX277063/SRX277063.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:09:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX277063/SRX277063.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:09:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX277063/SRX277063.20_summits.bed INFO @ Mon, 12 Aug 2019 18:09:20: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (53 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:09:21: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:09:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX277063/SRX277063.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:09:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX277063/SRX277063.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:09:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX277063/SRX277063.05_summits.bed INFO @ Mon, 12 Aug 2019 18:09:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (511 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:09:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX277063/SRX277063.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:09:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX277063/SRX277063.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:09:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX277063/SRX277063.10_summits.bed INFO @ Mon, 12 Aug 2019 18:09:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (194 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。