Job ID = 2589465 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,149,239 reads read : 4,149,239 reads written : 4,149,239 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR496304.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: 00:00:38 4149239 reads; of these: 4149239 (100.00%) were unpaired; of these: 1667361 (40.18%) aligned 0 times 2077835 (50.08%) aligned exactly 1 time 404043 (9.74%) aligned >1 times 59.82% overall alignment rate Time searching: 00:00:38 Overall time: 00:00:38 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] 111071 / 2481878 = 0.0448 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 17:44:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX147627/SRX147627.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX147627/SRX147627.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX147627/SRX147627.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX147627/SRX147627.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 17:44:55: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:44:55: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:44:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX147627/SRX147627.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX147627/SRX147627.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX147627/SRX147627.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX147627/SRX147627.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 17:44:56: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:44:56: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:44:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX147627/SRX147627.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX147627/SRX147627.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX147627/SRX147627.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX147627/SRX147627.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 17:44:57: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:44:57: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:45:02: 1000000 INFO @ Mon, 12 Aug 2019 17:45:03: 1000000 INFO @ Mon, 12 Aug 2019 17:45:04: 1000000 INFO @ Mon, 12 Aug 2019 17:45:10: 2000000 INFO @ Mon, 12 Aug 2019 17:45:11: 2000000 INFO @ Mon, 12 Aug 2019 17:45:11: 2000000 INFO @ Mon, 12 Aug 2019 17:45:13: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:45:13: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:45:13: #1 total tags in treatment: 2370807 INFO @ Mon, 12 Aug 2019 17:45:13: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:45:13: #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 17:45:13: #1 tags after filtering in treatment: 2370807 INFO @ Mon, 12 Aug 2019 17:45:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:45:13: #1 finished! INFO @ Mon, 12 Aug 2019 17:45:13: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:45:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:45:13: #2 number of paired peaks: 397 WARNING @ Mon, 12 Aug 2019 17:45:13: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Mon, 12 Aug 2019 17:45:13: start model_add_line... INFO @ Mon, 12 Aug 2019 17:45:13: start X-correlation... INFO @ Mon, 12 Aug 2019 17:45:13: end of X-cor INFO @ Mon, 12 Aug 2019 17:45:13: #2 finished! INFO @ Mon, 12 Aug 2019 17:45:13: #2 predicted fragment length is 31 bps INFO @ Mon, 12 Aug 2019 17:45:13: #2 alternative fragment length(s) may be 4,31,512,554 bps INFO @ Mon, 12 Aug 2019 17:45:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX147627/SRX147627.05_model.r WARNING @ Mon, 12 Aug 2019 17:45:13: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:45:13: #2 You may need to consider one of the other alternative d(s): 4,31,512,554 WARNING @ Mon, 12 Aug 2019 17:45:13: #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 17:45:13: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:45:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:45:14: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:45:14: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:45:14: #1 total tags in treatment: 2370807 INFO @ Mon, 12 Aug 2019 17:45:14: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:45:14: #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 17:45:14: #1 tags after filtering in treatment: 2370807 INFO @ Mon, 12 Aug 2019 17:45:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:45:14: #1 finished! INFO @ Mon, 12 Aug 2019 17:45:14: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:45:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:45:14: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:45:14: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:45:14: #1 total tags in treatment: 2370807 INFO @ Mon, 12 Aug 2019 17:45:14: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:45:14: #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 17:45:14: #1 tags after filtering in treatment: 2370807 INFO @ Mon, 12 Aug 2019 17:45:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:45:14: #1 finished! INFO @ Mon, 12 Aug 2019 17:45:14: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:45:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:45:14: #2 number of paired peaks: 397 WARNING @ Mon, 12 Aug 2019 17:45:14: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Mon, 12 Aug 2019 17:45:14: start model_add_line... INFO @ Mon, 12 Aug 2019 17:45:14: start X-correlation... INFO @ Mon, 12 Aug 2019 17:45:14: end of X-cor INFO @ Mon, 12 Aug 2019 17:45:14: #2 finished! INFO @ Mon, 12 Aug 2019 17:45:14: #2 predicted fragment length is 31 bps INFO @ Mon, 12 Aug 2019 17:45:14: #2 alternative fragment length(s) may be 4,31,512,554 bps INFO @ Mon, 12 Aug 2019 17:45:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX147627/SRX147627.10_model.r WARNING @ Mon, 12 Aug 2019 17:45:14: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:45:14: #2 You may need to consider one of the other alternative d(s): 4,31,512,554 WARNING @ Mon, 12 Aug 2019 17:45:14: #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 17:45:14: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:45:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:45:14: #2 number of paired peaks: 397 WARNING @ Mon, 12 Aug 2019 17:45:14: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Mon, 12 Aug 2019 17:45:14: start model_add_line... INFO @ Mon, 12 Aug 2019 17:45:14: start X-correlation... INFO @ Mon, 12 Aug 2019 17:45:14: end of X-cor INFO @ Mon, 12 Aug 2019 17:45:14: #2 finished! INFO @ Mon, 12 Aug 2019 17:45:14: #2 predicted fragment length is 31 bps INFO @ Mon, 12 Aug 2019 17:45:14: #2 alternative fragment length(s) may be 4,31,512,554 bps INFO @ Mon, 12 Aug 2019 17:45:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX147627/SRX147627.20_model.r WARNING @ Mon, 12 Aug 2019 17:45:14: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:45:14: #2 You may need to consider one of the other alternative d(s): 4,31,512,554 WARNING @ Mon, 12 Aug 2019 17:45:14: #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 17:45:14: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:45:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:45:21: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:45:22: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:45:22: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:45:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX147627/SRX147627.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:45:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX147627/SRX147627.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:45:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX147627/SRX147627.05_summits.bed INFO @ Mon, 12 Aug 2019 17:45:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (283 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:45:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX147627/SRX147627.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:45:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX147627/SRX147627.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:45:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX147627/SRX147627.20_summits.bed INFO @ Mon, 12 Aug 2019 17:45:26: Done! INFO @ Mon, 12 Aug 2019 17:45:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX147627/SRX147627.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:45:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX147627/SRX147627.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:45:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX147627/SRX147627.10_summits.bed INFO @ Mon, 12 Aug 2019 17:45:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (24 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (108 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。