Job ID = 1293017 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,151,464 reads read : 26,302,928 reads written : 13,151,464 reads 0-length : 13,151,464 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: 00:04:07 13151464 reads; of these: 13151464 (100.00%) were unpaired; of these: 4291964 (32.63%) aligned 0 times 7400081 (56.27%) aligned exactly 1 time 1459419 (11.10%) aligned >1 times 67.37% overall alignment rate Time searching: 00:04:07 Overall time: 00:04:07 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] 2299904 / 8859500 = 0.2596 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 21:35:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020788/SRX5020788.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020788/SRX5020788.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020788/SRX5020788.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020788/SRX5020788.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 21:35:14: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:35:14: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:35:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020788/SRX5020788.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020788/SRX5020788.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020788/SRX5020788.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020788/SRX5020788.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 21:35:14: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:35:14: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:35:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020788/SRX5020788.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020788/SRX5020788.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020788/SRX5020788.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020788/SRX5020788.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 21:35:14: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:35:14: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:35:22: 1000000 INFO @ Sun, 02 Jun 2019 21:35:22: 1000000 INFO @ Sun, 02 Jun 2019 21:35:23: 1000000 INFO @ Sun, 02 Jun 2019 21:35:30: 2000000 INFO @ Sun, 02 Jun 2019 21:35:30: 2000000 INFO @ Sun, 02 Jun 2019 21:35:32: 2000000 INFO @ Sun, 02 Jun 2019 21:35:37: 3000000 INFO @ Sun, 02 Jun 2019 21:35:37: 3000000 INFO @ Sun, 02 Jun 2019 21:35:41: 3000000 INFO @ Sun, 02 Jun 2019 21:35:45: 4000000 INFO @ Sun, 02 Jun 2019 21:35:45: 4000000 INFO @ Sun, 02 Jun 2019 21:35:50: 4000000 INFO @ Sun, 02 Jun 2019 21:35:52: 5000000 INFO @ Sun, 02 Jun 2019 21:35:53: 5000000 INFO @ Sun, 02 Jun 2019 21:35:59: 5000000 INFO @ Sun, 02 Jun 2019 21:36:00: 6000000 INFO @ Sun, 02 Jun 2019 21:36:00: 6000000 INFO @ Sun, 02 Jun 2019 21:36:04: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 21:36:04: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 21:36:04: #1 total tags in treatment: 6559596 INFO @ Sun, 02 Jun 2019 21:36:04: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:36:04: #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 21:36:04: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 21:36:04: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 21:36:04: #1 total tags in treatment: 6559596 INFO @ Sun, 02 Jun 2019 21:36:04: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:36:04: #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 21:36:04: #1 tags after filtering in treatment: 6559596 INFO @ Sun, 02 Jun 2019 21:36:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:36:04: #1 finished! INFO @ Sun, 02 Jun 2019 21:36:04: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:36:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:36:05: #1 tags after filtering in treatment: 6559596 INFO @ Sun, 02 Jun 2019 21:36:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:36:05: #1 finished! INFO @ Sun, 02 Jun 2019 21:36:05: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:36:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:36:05: #2 number of paired peaks: 475 WARNING @ Sun, 02 Jun 2019 21:36:05: Fewer paired peaks (475) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 475 pairs to build model! INFO @ Sun, 02 Jun 2019 21:36:05: start model_add_line... INFO @ Sun, 02 Jun 2019 21:36:05: #2 number of paired peaks: 475 WARNING @ Sun, 02 Jun 2019 21:36:05: Fewer paired peaks (475) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 475 pairs to build model! INFO @ Sun, 02 Jun 2019 21:36:05: start model_add_line... INFO @ Sun, 02 Jun 2019 21:36:05: start X-correlation... INFO @ Sun, 02 Jun 2019 21:36:05: end of X-cor INFO @ Sun, 02 Jun 2019 21:36:05: #2 finished! INFO @ Sun, 02 Jun 2019 21:36:05: #2 predicted fragment length is 77 bps INFO @ Sun, 02 Jun 2019 21:36:05: #2 alternative fragment length(s) may be 77,562 bps INFO @ Sun, 02 Jun 2019 21:36:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020788/SRX5020788.20_model.r WARNING @ Sun, 02 Jun 2019 21:36:05: #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 21:36:05: #2 You may need to consider one of the other alternative d(s): 77,562 WARNING @ Sun, 02 Jun 2019 21:36:05: #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 21:36:05: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:36:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:36:05: start X-correlation... INFO @ Sun, 02 Jun 2019 21:36:05: end of X-cor INFO @ Sun, 02 Jun 2019 21:36:05: #2 finished! INFO @ Sun, 02 Jun 2019 21:36:05: #2 predicted fragment length is 77 bps INFO @ Sun, 02 Jun 2019 21:36:05: #2 alternative fragment length(s) may be 77,562 bps INFO @ Sun, 02 Jun 2019 21:36:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020788/SRX5020788.05_model.r WARNING @ Sun, 02 Jun 2019 21:36:05: #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 21:36:05: #2 You may need to consider one of the other alternative d(s): 77,562 WARNING @ Sun, 02 Jun 2019 21:36:05: #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 21:36:05: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:36:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:36:08: 6000000 INFO @ Sun, 02 Jun 2019 21:36:13: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 21:36:13: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 21:36:13: #1 total tags in treatment: 6559596 INFO @ Sun, 02 Jun 2019 21:36:13: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:36:13: #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 21:36:13: #1 tags after filtering in treatment: 6559596 INFO @ Sun, 02 Jun 2019 21:36:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:36:13: #1 finished! INFO @ Sun, 02 Jun 2019 21:36:13: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:36:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:36:13: #2 number of paired peaks: 475 WARNING @ Sun, 02 Jun 2019 21:36:13: Fewer paired peaks (475) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 475 pairs to build model! INFO @ Sun, 02 Jun 2019 21:36:13: start model_add_line... INFO @ Sun, 02 Jun 2019 21:36:14: start X-correlation... INFO @ Sun, 02 Jun 2019 21:36:14: end of X-cor INFO @ Sun, 02 Jun 2019 21:36:14: #2 finished! INFO @ Sun, 02 Jun 2019 21:36:14: #2 predicted fragment length is 77 bps INFO @ Sun, 02 Jun 2019 21:36:14: #2 alternative fragment length(s) may be 77,562 bps INFO @ Sun, 02 Jun 2019 21:36:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020788/SRX5020788.10_model.r WARNING @ Sun, 02 Jun 2019 21:36:14: #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 21:36:14: #2 You may need to consider one of the other alternative d(s): 77,562 WARNING @ Sun, 02 Jun 2019 21:36:14: #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 21:36:14: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:36:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:36:24: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:36:24: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:36:33: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:36:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020788/SRX5020788.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:36:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020788/SRX5020788.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:36:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020788/SRX5020788.20_summits.bed INFO @ Sun, 02 Jun 2019 21:36:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (252 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:36:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020788/SRX5020788.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:36:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020788/SRX5020788.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:36:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020788/SRX5020788.05_summits.bed INFO @ Sun, 02 Jun 2019 21:36:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1360 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:36:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020788/SRX5020788.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:36:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020788/SRX5020788.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:36:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020788/SRX5020788.10_summits.bed INFO @ Sun, 02 Jun 2019 21:36:42: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (657 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。