Job ID = 2589673 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,008,664 reads read : 5,008,664 reads written : 5,008,664 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947273.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: 00:00:30 5008664 reads; of these: 5008664 (100.00%) were unpaired; of these: 3080529 (61.50%) aligned 0 times 1594233 (31.83%) aligned exactly 1 time 333902 (6.67%) aligned >1 times 38.50% overall alignment rate Time searching: 00:00:30 Overall time: 00:00:30 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] 87372 / 1928135 = 0.0453 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 18:13:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331050/SRX331050.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331050/SRX331050.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331050/SRX331050.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331050/SRX331050.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 18:13:06: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:13:06: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:13:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331050/SRX331050.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331050/SRX331050.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331050/SRX331050.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331050/SRX331050.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 18:13:06: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:13:06: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:13:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331050/SRX331050.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331050/SRX331050.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331050/SRX331050.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331050/SRX331050.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 18:13:07: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:13:07: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:13:14: 1000000 INFO @ Mon, 12 Aug 2019 18:13:15: 1000000 INFO @ Mon, 12 Aug 2019 18:13:16: 1000000 INFO @ Mon, 12 Aug 2019 18:13:21: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:13:21: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:13:21: #1 total tags in treatment: 1840763 INFO @ Mon, 12 Aug 2019 18:13:21: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:13:21: #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 18:13:21: #1 tags after filtering in treatment: 1840763 INFO @ Mon, 12 Aug 2019 18:13:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:13:21: #1 finished! INFO @ Mon, 12 Aug 2019 18:13:21: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:13:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:13:22: #2 number of paired peaks: 462 WARNING @ Mon, 12 Aug 2019 18:13:22: Fewer paired peaks (462) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 462 pairs to build model! INFO @ Mon, 12 Aug 2019 18:13:22: start model_add_line... INFO @ Mon, 12 Aug 2019 18:13:22: start X-correlation... INFO @ Mon, 12 Aug 2019 18:13:22: end of X-cor INFO @ Mon, 12 Aug 2019 18:13:22: #2 finished! INFO @ Mon, 12 Aug 2019 18:13:22: #2 predicted fragment length is 43 bps INFO @ Mon, 12 Aug 2019 18:13:22: #2 alternative fragment length(s) may be 43,540,559,593 bps INFO @ Mon, 12 Aug 2019 18:13:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331050/SRX331050.05_model.r WARNING @ Mon, 12 Aug 2019 18:13:22: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:13:22: #2 You may need to consider one of the other alternative d(s): 43,540,559,593 WARNING @ Mon, 12 Aug 2019 18:13:22: #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 18:13:22: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:13:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:13:22: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:13:22: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:13:22: #1 total tags in treatment: 1840763 INFO @ Mon, 12 Aug 2019 18:13:22: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:13:22: #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 18:13:22: #1 tags after filtering in treatment: 1840763 INFO @ Mon, 12 Aug 2019 18:13:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:13:22: #1 finished! INFO @ Mon, 12 Aug 2019 18:13:22: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:13:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:13:22: #2 number of paired peaks: 462 WARNING @ Mon, 12 Aug 2019 18:13:22: Fewer paired peaks (462) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 462 pairs to build model! INFO @ Mon, 12 Aug 2019 18:13:22: start model_add_line... INFO @ Mon, 12 Aug 2019 18:13:22: start X-correlation... INFO @ Mon, 12 Aug 2019 18:13:22: end of X-cor INFO @ Mon, 12 Aug 2019 18:13:22: #2 finished! INFO @ Mon, 12 Aug 2019 18:13:22: #2 predicted fragment length is 43 bps INFO @ Mon, 12 Aug 2019 18:13:22: #2 alternative fragment length(s) may be 43,540,559,593 bps INFO @ Mon, 12 Aug 2019 18:13:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331050/SRX331050.10_model.r WARNING @ Mon, 12 Aug 2019 18:13:22: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:13:22: #2 You may need to consider one of the other alternative d(s): 43,540,559,593 WARNING @ Mon, 12 Aug 2019 18:13:22: #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 18:13:22: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:13:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:13:22: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:13:22: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:13:22: #1 total tags in treatment: 1840763 INFO @ Mon, 12 Aug 2019 18:13:22: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:13:22: #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 18:13:22: #1 tags after filtering in treatment: 1840763 INFO @ Mon, 12 Aug 2019 18:13:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:13:22: #1 finished! INFO @ Mon, 12 Aug 2019 18:13:22: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:13:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:13:23: #2 number of paired peaks: 462 WARNING @ Mon, 12 Aug 2019 18:13:23: Fewer paired peaks (462) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 462 pairs to build model! INFO @ Mon, 12 Aug 2019 18:13:23: start model_add_line... INFO @ Mon, 12 Aug 2019 18:13:23: start X-correlation... INFO @ Mon, 12 Aug 2019 18:13:23: end of X-cor INFO @ Mon, 12 Aug 2019 18:13:23: #2 finished! INFO @ Mon, 12 Aug 2019 18:13:23: #2 predicted fragment length is 43 bps INFO @ Mon, 12 Aug 2019 18:13:23: #2 alternative fragment length(s) may be 43,540,559,593 bps INFO @ Mon, 12 Aug 2019 18:13:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331050/SRX331050.20_model.r WARNING @ Mon, 12 Aug 2019 18:13:23: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:13:23: #2 You may need to consider one of the other alternative d(s): 43,540,559,593 WARNING @ Mon, 12 Aug 2019 18:13:23: #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 18:13:23: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:13:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:13:27: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:13:28: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:13:28: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:13:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331050/SRX331050.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:13:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331050/SRX331050.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:13:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331050/SRX331050.05_summits.bed INFO @ Mon, 12 Aug 2019 18:13:30: Done! INFO @ Mon, 12 Aug 2019 18:13:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331050/SRX331050.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:13:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331050/SRX331050.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:13:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331050/SRX331050.10_summits.bed INFO @ Mon, 12 Aug 2019 18:13:31: Done! pass1 - making usageList (6 chroms): 1 millis pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (151 records, 4 fields)pass2 - checking and writing primary data (318 records, 4 fields): 3 millis : 4 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:13:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331050/SRX331050.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:13:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331050/SRX331050.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:13:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331050/SRX331050.20_summits.bed INFO @ Mon, 12 Aug 2019 18:13:32: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (40 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。