Job ID = 2589341 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,537,084 reads read : 4,537,084 reads written : 4,537,084 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR217422.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: 00:00:47 4537084 reads; of these: 4537084 (100.00%) were unpaired; of these: 705619 (15.55%) aligned 0 times 3222012 (71.02%) aligned exactly 1 time 609453 (13.43%) aligned >1 times 84.45% overall alignment rate Time searching: 00:00:47 Overall time: 00:00:47 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] 193998 / 3831465 = 0.0506 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 17:28:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX065716/SRX065716.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX065716/SRX065716.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX065716/SRX065716.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX065716/SRX065716.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 17:28:12: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:28:12: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:28:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX065716/SRX065716.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX065716/SRX065716.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX065716/SRX065716.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX065716/SRX065716.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 17:28:14: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:28:14: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:28:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX065716/SRX065716.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX065716/SRX065716.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX065716/SRX065716.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX065716/SRX065716.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 17:28:14: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:28:14: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:28:19: 1000000 INFO @ Mon, 12 Aug 2019 17:28:22: 1000000 INFO @ Mon, 12 Aug 2019 17:28:23: 1000000 INFO @ Mon, 12 Aug 2019 17:28:26: 2000000 INFO @ Mon, 12 Aug 2019 17:28:29: 2000000 INFO @ Mon, 12 Aug 2019 17:28:32: 2000000 INFO @ Mon, 12 Aug 2019 17:28:33: 3000000 INFO @ Mon, 12 Aug 2019 17:28:37: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:28:37: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:28:37: #1 total tags in treatment: 3637467 INFO @ Mon, 12 Aug 2019 17:28:37: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:28:37: #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 17:28:37: #1 tags after filtering in treatment: 3637467 INFO @ Mon, 12 Aug 2019 17:28:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:28:37: #1 finished! INFO @ Mon, 12 Aug 2019 17:28:37: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:28:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:28:37: #2 number of paired peaks: 387 WARNING @ Mon, 12 Aug 2019 17:28:37: Fewer paired peaks (387) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 387 pairs to build model! INFO @ Mon, 12 Aug 2019 17:28:37: start model_add_line... INFO @ Mon, 12 Aug 2019 17:28:37: start X-correlation... INFO @ Mon, 12 Aug 2019 17:28:37: end of X-cor INFO @ Mon, 12 Aug 2019 17:28:37: #2 finished! INFO @ Mon, 12 Aug 2019 17:28:37: #2 predicted fragment length is 33 bps INFO @ Mon, 12 Aug 2019 17:28:37: #2 alternative fragment length(s) may be 4,33,553,567,587 bps INFO @ Mon, 12 Aug 2019 17:28:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX065716/SRX065716.05_model.r WARNING @ Mon, 12 Aug 2019 17:28:37: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:28:37: #2 You may need to consider one of the other alternative d(s): 4,33,553,567,587 WARNING @ Mon, 12 Aug 2019 17:28:37: #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 17:28:37: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:28:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:28:37: 3000000 INFO @ Mon, 12 Aug 2019 17:28:42: 3000000 INFO @ Mon, 12 Aug 2019 17:28:42: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:28:42: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:28:42: #1 total tags in treatment: 3637467 INFO @ Mon, 12 Aug 2019 17:28:42: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:28:42: #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 17:28:42: #1 tags after filtering in treatment: 3637467 INFO @ Mon, 12 Aug 2019 17:28:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:28:42: #1 finished! INFO @ Mon, 12 Aug 2019 17:28:42: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:28:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:28:43: #2 number of paired peaks: 387 WARNING @ Mon, 12 Aug 2019 17:28:43: Fewer paired peaks (387) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 387 pairs to build model! INFO @ Mon, 12 Aug 2019 17:28:43: start model_add_line... INFO @ Mon, 12 Aug 2019 17:28:43: start X-correlation... INFO @ Mon, 12 Aug 2019 17:28:43: end of X-cor INFO @ Mon, 12 Aug 2019 17:28:43: #2 finished! INFO @ Mon, 12 Aug 2019 17:28:43: #2 predicted fragment length is 33 bps INFO @ Mon, 12 Aug 2019 17:28:43: #2 alternative fragment length(s) may be 4,33,553,567,587 bps INFO @ Mon, 12 Aug 2019 17:28:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX065716/SRX065716.10_model.r WARNING @ Mon, 12 Aug 2019 17:28:43: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:28:43: #2 You may need to consider one of the other alternative d(s): 4,33,553,567,587 WARNING @ Mon, 12 Aug 2019 17:28:43: #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 17:28:43: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:28:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:28:48: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:28:48: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:28:48: #1 total tags in treatment: 3637467 INFO @ Mon, 12 Aug 2019 17:28:48: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:28:48: #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 17:28:48: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:28:48: #1 tags after filtering in treatment: 3637467 INFO @ Mon, 12 Aug 2019 17:28:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:28:48: #1 finished! INFO @ Mon, 12 Aug 2019 17:28:48: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:28:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:28:48: #2 number of paired peaks: 387 WARNING @ Mon, 12 Aug 2019 17:28:48: Fewer paired peaks (387) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 387 pairs to build model! INFO @ Mon, 12 Aug 2019 17:28:48: start model_add_line... INFO @ Mon, 12 Aug 2019 17:28:48: start X-correlation... INFO @ Mon, 12 Aug 2019 17:28:48: end of X-cor INFO @ Mon, 12 Aug 2019 17:28:48: #2 finished! INFO @ Mon, 12 Aug 2019 17:28:48: #2 predicted fragment length is 33 bps INFO @ Mon, 12 Aug 2019 17:28:48: #2 alternative fragment length(s) may be 4,33,553,567,587 bps INFO @ Mon, 12 Aug 2019 17:28:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX065716/SRX065716.20_model.r WARNING @ Mon, 12 Aug 2019 17:28:48: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:28:48: #2 You may need to consider one of the other alternative d(s): 4,33,553,567,587 WARNING @ Mon, 12 Aug 2019 17:28:48: #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 17:28:48: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:28:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:28:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX065716/SRX065716.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:28:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX065716/SRX065716.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:28:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX065716/SRX065716.05_summits.bed INFO @ Mon, 12 Aug 2019 17:28:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (365 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:28:53: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:28:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX065716/SRX065716.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:28:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX065716/SRX065716.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:28:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX065716/SRX065716.10_summits.bed INFO @ Mon, 12 Aug 2019 17:28:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (150 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:28:59: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:29:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX065716/SRX065716.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:29:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX065716/SRX065716.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:29:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX065716/SRX065716.20_summits.bed INFO @ Mon, 12 Aug 2019 17:29:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (39 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。