Job ID = 1292324 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,598,392 reads read : 13,598,392 reads written : 13,598,392 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: 00:03:14 13598392 reads; of these: 13598392 (100.00%) were unpaired; of these: 978371 (7.19%) aligned 0 times 10971727 (80.68%) aligned exactly 1 time 1648294 (12.12%) aligned >1 times 92.81% overall alignment rate Time searching: 00:03:14 Overall time: 00:03:14 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_sort_core] merging from 8 files... [bam_rmdupse_core] 6982315 / 12620021 = 0.5533 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 17:58:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331348/SRX331348.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331348/SRX331348.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331348/SRX331348.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331348/SRX331348.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 17:58:03: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:58:03: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:58:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331348/SRX331348.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331348/SRX331348.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331348/SRX331348.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331348/SRX331348.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 17:58:03: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:58:03: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:58:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331348/SRX331348.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331348/SRX331348.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331348/SRX331348.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331348/SRX331348.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 17:58:03: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:58:03: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:58:11: 1000000 INFO @ Sun, 02 Jun 2019 17:58:12: 1000000 INFO @ Sun, 02 Jun 2019 17:58:12: 1000000 INFO @ Sun, 02 Jun 2019 17:58:19: 2000000 INFO @ Sun, 02 Jun 2019 17:58:20: 2000000 INFO @ Sun, 02 Jun 2019 17:58:21: 2000000 INFO @ Sun, 02 Jun 2019 17:58:27: 3000000 INFO @ Sun, 02 Jun 2019 17:58:28: 3000000 INFO @ Sun, 02 Jun 2019 17:58:29: 3000000 INFO @ Sun, 02 Jun 2019 17:58:35: 4000000 INFO @ Sun, 02 Jun 2019 17:58:36: 4000000 INFO @ Sun, 02 Jun 2019 17:58:38: 4000000 INFO @ Sun, 02 Jun 2019 17:58:43: 5000000 INFO @ Sun, 02 Jun 2019 17:58:44: 5000000 INFO @ Sun, 02 Jun 2019 17:58:46: 5000000 INFO @ Sun, 02 Jun 2019 17:58:48: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 17:58:48: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 17:58:48: #1 total tags in treatment: 5637706 INFO @ Sun, 02 Jun 2019 17:58:48: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:58:48: #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 17:58:48: #1 tags after filtering in treatment: 5637706 INFO @ Sun, 02 Jun 2019 17:58:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:58:48: #1 finished! INFO @ Sun, 02 Jun 2019 17:58:48: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:58:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:58:49: #2 number of paired peaks: 523 WARNING @ Sun, 02 Jun 2019 17:58:49: Fewer paired peaks (523) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 523 pairs to build model! INFO @ Sun, 02 Jun 2019 17:58:49: start model_add_line... INFO @ Sun, 02 Jun 2019 17:58:49: start X-correlation... INFO @ Sun, 02 Jun 2019 17:58:49: end of X-cor INFO @ Sun, 02 Jun 2019 17:58:49: #2 finished! INFO @ Sun, 02 Jun 2019 17:58:49: #2 predicted fragment length is 53 bps INFO @ Sun, 02 Jun 2019 17:58:49: #2 alternative fragment length(s) may be 4,53,579 bps INFO @ Sun, 02 Jun 2019 17:58:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331348/SRX331348.05_model.r WARNING @ Sun, 02 Jun 2019 17:58:49: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:58:49: #2 You may need to consider one of the other alternative d(s): 4,53,579 WARNING @ Sun, 02 Jun 2019 17:58:49: #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 17:58:49: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:58:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:58:49: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 17:58:49: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 17:58:49: #1 total tags in treatment: 5637706 INFO @ Sun, 02 Jun 2019 17:58:49: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:58:49: #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 17:58:49: #1 tags after filtering in treatment: 5637706 INFO @ Sun, 02 Jun 2019 17:58:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:58:49: #1 finished! INFO @ Sun, 02 Jun 2019 17:58:49: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:58:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:58:50: #2 number of paired peaks: 523 WARNING @ Sun, 02 Jun 2019 17:58:50: Fewer paired peaks (523) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 523 pairs to build model! INFO @ Sun, 02 Jun 2019 17:58:50: start model_add_line... INFO @ Sun, 02 Jun 2019 17:58:50: start X-correlation... INFO @ Sun, 02 Jun 2019 17:58:50: end of X-cor INFO @ Sun, 02 Jun 2019 17:58:50: #2 finished! INFO @ Sun, 02 Jun 2019 17:58:50: #2 predicted fragment length is 53 bps INFO @ Sun, 02 Jun 2019 17:58:50: #2 alternative fragment length(s) may be 4,53,579 bps INFO @ Sun, 02 Jun 2019 17:58:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331348/SRX331348.20_model.r WARNING @ Sun, 02 Jun 2019 17:58:50: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:58:50: #2 You may need to consider one of the other alternative d(s): 4,53,579 WARNING @ Sun, 02 Jun 2019 17:58:50: #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 17:58:50: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:58:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:58:51: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 17:58:51: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 17:58:51: #1 total tags in treatment: 5637706 INFO @ Sun, 02 Jun 2019 17:58:51: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:58:51: #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 17:58:51: #1 tags after filtering in treatment: 5637706 INFO @ Sun, 02 Jun 2019 17:58:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:58:51: #1 finished! INFO @ Sun, 02 Jun 2019 17:58:51: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:58:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:58:52: #2 number of paired peaks: 523 WARNING @ Sun, 02 Jun 2019 17:58:52: Fewer paired peaks (523) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 523 pairs to build model! INFO @ Sun, 02 Jun 2019 17:58:52: start model_add_line... INFO @ Sun, 02 Jun 2019 17:58:52: start X-correlation... INFO @ Sun, 02 Jun 2019 17:58:52: end of X-cor INFO @ Sun, 02 Jun 2019 17:58:52: #2 finished! INFO @ Sun, 02 Jun 2019 17:58:52: #2 predicted fragment length is 53 bps INFO @ Sun, 02 Jun 2019 17:58:52: #2 alternative fragment length(s) may be 4,53,579 bps INFO @ Sun, 02 Jun 2019 17:58:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331348/SRX331348.10_model.r WARNING @ Sun, 02 Jun 2019 17:58:52: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:58:52: #2 You may need to consider one of the other alternative d(s): 4,53,579 WARNING @ Sun, 02 Jun 2019 17:58:52: #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 17:58:52: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:58:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:59:05: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:59:06: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:59:09: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:59:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331348/SRX331348.05_peaks.xls INFO @ Sun, 02 Jun 2019 17:59:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331348/SRX331348.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:59:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331348/SRX331348.05_summits.bed INFO @ Sun, 02 Jun 2019 17:59:14: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1014 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:59:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331348/SRX331348.20_peaks.xls INFO @ Sun, 02 Jun 2019 17:59:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331348/SRX331348.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:59:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331348/SRX331348.20_summits.bed INFO @ Sun, 02 Jun 2019 17:59:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (127 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:59:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331348/SRX331348.10_peaks.xls INFO @ Sun, 02 Jun 2019 17:59:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331348/SRX331348.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:59:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331348/SRX331348.10_summits.bed INFO @ Sun, 02 Jun 2019 17:59:17: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (387 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。