Job ID = 2589432 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,071,171 reads read : 3,071,171 reads written : 3,071,171 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR494673.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: 00:00:23 3071171 reads; of these: 3071171 (100.00%) were unpaired; of these: 1829425 (59.57%) aligned 0 times 1022950 (33.31%) aligned exactly 1 time 218796 (7.12%) aligned >1 times 40.43% overall alignment rate Time searching: 00:00:23 Overall time: 00:00:23 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] 78641 / 1241746 = 0.0633 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 17:39:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX146505/SRX146505.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX146505/SRX146505.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX146505/SRX146505.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX146505/SRX146505.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 17:39:30: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:39:30: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:39:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX146505/SRX146505.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX146505/SRX146505.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX146505/SRX146505.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX146505/SRX146505.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 17:39:31: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:39:31: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:39:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX146505/SRX146505.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX146505/SRX146505.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX146505/SRX146505.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX146505/SRX146505.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 17:39:32: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:39:32: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:39:38: 1000000 INFO @ Mon, 12 Aug 2019 17:39:39: 1000000 INFO @ Mon, 12 Aug 2019 17:39:39: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:39:39: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:39:39: #1 total tags in treatment: 1163105 INFO @ Mon, 12 Aug 2019 17:39:39: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:39:39: #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 17:39:39: #1 tags after filtering in treatment: 1163105 INFO @ Mon, 12 Aug 2019 17:39:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:39:39: #1 finished! INFO @ Mon, 12 Aug 2019 17:39:39: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:39:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:39:39: #2 number of paired peaks: 517 WARNING @ Mon, 12 Aug 2019 17:39:39: Fewer paired peaks (517) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 517 pairs to build model! INFO @ Mon, 12 Aug 2019 17:39:39: start model_add_line... INFO @ Mon, 12 Aug 2019 17:39:39: start X-correlation... INFO @ Mon, 12 Aug 2019 17:39:39: end of X-cor INFO @ Mon, 12 Aug 2019 17:39:39: #2 finished! INFO @ Mon, 12 Aug 2019 17:39:39: #2 predicted fragment length is 31 bps INFO @ Mon, 12 Aug 2019 17:39:39: #2 alternative fragment length(s) may be 31,89,135,147,508 bps INFO @ Mon, 12 Aug 2019 17:39:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX146505/SRX146505.05_model.r WARNING @ Mon, 12 Aug 2019 17:39:39: #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 17:39:39: #2 You may need to consider one of the other alternative d(s): 31,89,135,147,508 WARNING @ Mon, 12 Aug 2019 17:39:39: #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 17:39:39: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:39:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:39:40: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:39:40: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:39:40: #1 total tags in treatment: 1163105 INFO @ Mon, 12 Aug 2019 17:39:40: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:39:40: #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 17:39:40: #1 tags after filtering in treatment: 1163105 INFO @ Mon, 12 Aug 2019 17:39:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:39:40: #1 finished! INFO @ Mon, 12 Aug 2019 17:39:40: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:39:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:39:40: #2 number of paired peaks: 517 WARNING @ Mon, 12 Aug 2019 17:39:40: Fewer paired peaks (517) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 517 pairs to build model! INFO @ Mon, 12 Aug 2019 17:39:40: start model_add_line... INFO @ Mon, 12 Aug 2019 17:39:40: start X-correlation... INFO @ Mon, 12 Aug 2019 17:39:40: end of X-cor INFO @ Mon, 12 Aug 2019 17:39:40: #2 finished! INFO @ Mon, 12 Aug 2019 17:39:40: #2 predicted fragment length is 31 bps INFO @ Mon, 12 Aug 2019 17:39:40: #2 alternative fragment length(s) may be 31,89,135,147,508 bps INFO @ Mon, 12 Aug 2019 17:39:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX146505/SRX146505.10_model.r WARNING @ Mon, 12 Aug 2019 17:39:40: #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 17:39:40: #2 You may need to consider one of the other alternative d(s): 31,89,135,147,508 WARNING @ Mon, 12 Aug 2019 17:39:40: #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 17:39:40: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:39:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:39:41: 1000000 INFO @ Mon, 12 Aug 2019 17:39:43: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:39:43: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:39:43: #1 total tags in treatment: 1163105 INFO @ Mon, 12 Aug 2019 17:39:43: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:39:43: #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 17:39:43: #1 tags after filtering in treatment: 1163105 INFO @ Mon, 12 Aug 2019 17:39:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:39:43: #1 finished! INFO @ Mon, 12 Aug 2019 17:39:43: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:39:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:39:43: #2 number of paired peaks: 517 WARNING @ Mon, 12 Aug 2019 17:39:43: Fewer paired peaks (517) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 517 pairs to build model! INFO @ Mon, 12 Aug 2019 17:39:43: start model_add_line... INFO @ Mon, 12 Aug 2019 17:39:43: start X-correlation... INFO @ Mon, 12 Aug 2019 17:39:43: end of X-cor INFO @ Mon, 12 Aug 2019 17:39:43: #2 finished! INFO @ Mon, 12 Aug 2019 17:39:43: #2 predicted fragment length is 31 bps INFO @ Mon, 12 Aug 2019 17:39:43: #2 alternative fragment length(s) may be 31,89,135,147,508 bps INFO @ Mon, 12 Aug 2019 17:39:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX146505/SRX146505.20_model.r WARNING @ Mon, 12 Aug 2019 17:39:43: #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 17:39:43: #2 You may need to consider one of the other alternative d(s): 31,89,135,147,508 WARNING @ Mon, 12 Aug 2019 17:39:43: #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 17:39:43: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:39:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:39:43: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:39:44: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:39:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX146505/SRX146505.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:39:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX146505/SRX146505.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:39:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX146505/SRX146505.05_summits.bed INFO @ Mon, 12 Aug 2019 17:39:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (187 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:39:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX146505/SRX146505.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:39:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX146505/SRX146505.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:39:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX146505/SRX146505.10_summits.bed INFO @ Mon, 12 Aug 2019 17:39:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (70 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:39:46: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 12 Aug 2019 17:39:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX146505/SRX146505.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:39:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX146505/SRX146505.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:39:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX146505/SRX146505.20_summits.bed INFO @ Mon, 12 Aug 2019 17:39:48: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (7 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。