Job ID = 1292907 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,748,012 reads read : 19,496,024 reads written : 9,748,012 reads 0-length : 9,748,012 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:03:22 9748012 reads; of these: 9748012 (100.00%) were unpaired; of these: 180070 (1.85%) aligned 0 times 8134442 (83.45%) aligned exactly 1 time 1433500 (14.71%) aligned >1 times 98.15% overall alignment rate Time searching: 00:03:22 Overall time: 00:03:22 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] 560612 / 9567942 = 0.0586 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 @ Sun, 02 Jun 2019 21:13:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020706/SRX5020706.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020706/SRX5020706.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020706/SRX5020706.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020706/SRX5020706.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 @ Sun, 02 Jun 2019 21:13:15: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:13:15: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:13:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020706/SRX5020706.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020706/SRX5020706.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020706/SRX5020706.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020706/SRX5020706.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 @ Sun, 02 Jun 2019 21:13:15: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:13:15: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:13:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020706/SRX5020706.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020706/SRX5020706.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020706/SRX5020706.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020706/SRX5020706.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 @ Sun, 02 Jun 2019 21:13:15: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:13:15: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:13:24: 1000000 INFO @ Sun, 02 Jun 2019 21:13:26: 1000000 INFO @ Sun, 02 Jun 2019 21:13:26: 1000000 INFO @ Sun, 02 Jun 2019 21:13:34: 2000000 INFO @ Sun, 02 Jun 2019 21:13:36: 2000000 INFO @ Sun, 02 Jun 2019 21:13:36: 2000000 INFO @ Sun, 02 Jun 2019 21:13:44: 3000000 INFO @ Sun, 02 Jun 2019 21:13:47: 3000000 INFO @ Sun, 02 Jun 2019 21:13:47: 3000000 INFO @ Sun, 02 Jun 2019 21:13:53: 4000000 INFO @ Sun, 02 Jun 2019 21:13:58: 4000000 INFO @ Sun, 02 Jun 2019 21:13:58: 4000000 INFO @ Sun, 02 Jun 2019 21:14:01: 5000000 INFO @ Sun, 02 Jun 2019 21:14:08: 5000000 INFO @ Sun, 02 Jun 2019 21:14:08: 5000000 INFO @ Sun, 02 Jun 2019 21:14:10: 6000000 INFO @ Sun, 02 Jun 2019 21:14:18: 6000000 INFO @ Sun, 02 Jun 2019 21:14:18: 6000000 INFO @ Sun, 02 Jun 2019 21:14:19: 7000000 INFO @ Sun, 02 Jun 2019 21:14:27: 8000000 INFO @ Sun, 02 Jun 2019 21:14:28: 7000000 INFO @ Sun, 02 Jun 2019 21:14:28: 7000000 INFO @ Sun, 02 Jun 2019 21:14:36: 9000000 INFO @ Sun, 02 Jun 2019 21:14:36: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 21:14:36: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 21:14:36: #1 total tags in treatment: 9007330 INFO @ Sun, 02 Jun 2019 21:14:36: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:14:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 21:14:36: #1 tags after filtering in treatment: 9007330 INFO @ Sun, 02 Jun 2019 21:14:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:14:36: #1 finished! INFO @ Sun, 02 Jun 2019 21:14:36: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:14:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:14:37: #2 number of paired peaks: 269 WARNING @ Sun, 02 Jun 2019 21:14:37: Fewer paired peaks (269) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 269 pairs to build model! INFO @ Sun, 02 Jun 2019 21:14:37: start model_add_line... INFO @ Sun, 02 Jun 2019 21:14:37: start X-correlation... INFO @ Sun, 02 Jun 2019 21:14:37: end of X-cor INFO @ Sun, 02 Jun 2019 21:14:37: #2 finished! INFO @ Sun, 02 Jun 2019 21:14:37: #2 predicted fragment length is 77 bps INFO @ Sun, 02 Jun 2019 21:14:37: #2 alternative fragment length(s) may be 77,540 bps INFO @ Sun, 02 Jun 2019 21:14:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020706/SRX5020706.10_model.r WARNING @ Sun, 02 Jun 2019 21:14:37: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:14:37: #2 You may need to consider one of the other alternative d(s): 77,540 WARNING @ Sun, 02 Jun 2019 21:14:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 21:14:37: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:14:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:14:38: 8000000 INFO @ Sun, 02 Jun 2019 21:14:38: 8000000 INFO @ Sun, 02 Jun 2019 21:14:47: 9000000 INFO @ Sun, 02 Jun 2019 21:14:47: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 21:14:47: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 21:14:47: #1 total tags in treatment: 9007330 INFO @ Sun, 02 Jun 2019 21:14:47: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:14:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 21:14:47: #1 tags after filtering in treatment: 9007330 INFO @ Sun, 02 Jun 2019 21:14:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:14:47: #1 finished! INFO @ Sun, 02 Jun 2019 21:14:47: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:14:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:14:48: 9000000 INFO @ Sun, 02 Jun 2019 21:14:48: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 21:14:48: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 21:14:48: #1 total tags in treatment: 9007330 INFO @ Sun, 02 Jun 2019 21:14:48: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:14:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 21:14:48: #1 tags after filtering in treatment: 9007330 INFO @ Sun, 02 Jun 2019 21:14:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:14:48: #1 finished! INFO @ Sun, 02 Jun 2019 21:14:48: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:14:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:14:48: #2 number of paired peaks: 269 WARNING @ Sun, 02 Jun 2019 21:14:48: Fewer paired peaks (269) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 269 pairs to build model! INFO @ Sun, 02 Jun 2019 21:14:48: start model_add_line... INFO @ Sun, 02 Jun 2019 21:14:48: start X-correlation... INFO @ Sun, 02 Jun 2019 21:14:48: end of X-cor INFO @ Sun, 02 Jun 2019 21:14:48: #2 finished! INFO @ Sun, 02 Jun 2019 21:14:48: #2 predicted fragment length is 77 bps INFO @ Sun, 02 Jun 2019 21:14:48: #2 alternative fragment length(s) may be 77,540 bps INFO @ Sun, 02 Jun 2019 21:14:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020706/SRX5020706.20_model.r WARNING @ Sun, 02 Jun 2019 21:14:48: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:14:48: #2 You may need to consider one of the other alternative d(s): 77,540 WARNING @ Sun, 02 Jun 2019 21:14:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 21:14:48: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:14:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:14:49: #2 number of paired peaks: 269 WARNING @ Sun, 02 Jun 2019 21:14:49: Fewer paired peaks (269) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 269 pairs to build model! INFO @ Sun, 02 Jun 2019 21:14:49: start model_add_line... INFO @ Sun, 02 Jun 2019 21:14:49: start X-correlation... INFO @ Sun, 02 Jun 2019 21:14:49: end of X-cor INFO @ Sun, 02 Jun 2019 21:14:49: #2 finished! INFO @ Sun, 02 Jun 2019 21:14:49: #2 predicted fragment length is 77 bps INFO @ Sun, 02 Jun 2019 21:14:49: #2 alternative fragment length(s) may be 77,540 bps INFO @ Sun, 02 Jun 2019 21:14:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020706/SRX5020706.05_model.r WARNING @ Sun, 02 Jun 2019 21:14:49: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:14:49: #2 You may need to consider one of the other alternative d(s): 77,540 WARNING @ Sun, 02 Jun 2019 21:14:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 21:14:49: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:14:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:15:03: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:15:15: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:15:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020706/SRX5020706.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:15:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020706/SRX5020706.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:15:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020706/SRX5020706.10_summits.bed INFO @ Sun, 02 Jun 2019 21:15:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (338 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:15:16: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:15:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020706/SRX5020706.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:15:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020706/SRX5020706.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:15:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020706/SRX5020706.20_summits.bed INFO @ Sun, 02 Jun 2019 21:15:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (191 records, 4 fields): 92 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:15:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020706/SRX5020706.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:15:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020706/SRX5020706.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:15:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020706/SRX5020706.05_summits.bed INFO @ Sun, 02 Jun 2019 21:15:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (518 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。