Job ID = 1293066 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,901,860 reads read : 12,901,860 reads written : 12,901,860 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: 00:03:16 12901860 reads; of these: 12901860 (100.00%) were unpaired; of these: 118205 (0.92%) aligned 0 times 10601459 (82.17%) aligned exactly 1 time 2182196 (16.91%) aligned >1 times 99.08% overall alignment rate Time searching: 00:03:16 Overall time: 00:03:16 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] 1011575 / 12783655 = 0.0791 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 21:45:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020828/SRX5020828.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020828/SRX5020828.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020828/SRX5020828.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020828/SRX5020828.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 21:45:09: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:45:09: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:45:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020828/SRX5020828.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020828/SRX5020828.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020828/SRX5020828.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020828/SRX5020828.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 21:45:09: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:45:09: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:45:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020828/SRX5020828.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020828/SRX5020828.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020828/SRX5020828.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020828/SRX5020828.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 21:45:09: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:45:09: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:45:20: 1000000 INFO @ Sun, 02 Jun 2019 21:45:20: 1000000 INFO @ Sun, 02 Jun 2019 21:45:20: 1000000 INFO @ Sun, 02 Jun 2019 21:45:29: 2000000 INFO @ Sun, 02 Jun 2019 21:45:30: 2000000 INFO @ Sun, 02 Jun 2019 21:45:30: 2000000 INFO @ Sun, 02 Jun 2019 21:45:39: 3000000 INFO @ Sun, 02 Jun 2019 21:45:41: 3000000 INFO @ Sun, 02 Jun 2019 21:45:41: 3000000 INFO @ Sun, 02 Jun 2019 21:45:49: 4000000 INFO @ Sun, 02 Jun 2019 21:45:50: 4000000 INFO @ Sun, 02 Jun 2019 21:45:50: 4000000 INFO @ Sun, 02 Jun 2019 21:45:58: 5000000 INFO @ Sun, 02 Jun 2019 21:46:00: 5000000 INFO @ Sun, 02 Jun 2019 21:46:01: 5000000 INFO @ Sun, 02 Jun 2019 21:46:08: 6000000 INFO @ Sun, 02 Jun 2019 21:46:10: 6000000 INFO @ Sun, 02 Jun 2019 21:46:10: 6000000 INFO @ Sun, 02 Jun 2019 21:46:17: 7000000 INFO @ Sun, 02 Jun 2019 21:46:20: 7000000 INFO @ Sun, 02 Jun 2019 21:46:20: 7000000 INFO @ Sun, 02 Jun 2019 21:46:26: 8000000 INFO @ Sun, 02 Jun 2019 21:46:30: 8000000 INFO @ Sun, 02 Jun 2019 21:46:30: 8000000 INFO @ Sun, 02 Jun 2019 21:46:35: 9000000 INFO @ Sun, 02 Jun 2019 21:46:39: 9000000 INFO @ Sun, 02 Jun 2019 21:46:39: 9000000 INFO @ Sun, 02 Jun 2019 21:46:44: 10000000 INFO @ Sun, 02 Jun 2019 21:46:48: 10000000 INFO @ Sun, 02 Jun 2019 21:46:49: 10000000 INFO @ Sun, 02 Jun 2019 21:46:53: 11000000 INFO @ Sun, 02 Jun 2019 21:46:58: 11000000 INFO @ Sun, 02 Jun 2019 21:46:58: 11000000 INFO @ Sun, 02 Jun 2019 21:47:00: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:47:00: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:47:00: #1 total tags in treatment: 11772080 INFO @ Sun, 02 Jun 2019 21:47:00: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:47:00: #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 21:47:00: #1 tags after filtering in treatment: 11772080 INFO @ Sun, 02 Jun 2019 21:47:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:47:00: #1 finished! INFO @ Sun, 02 Jun 2019 21:47:00: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:47:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:47:01: #2 number of paired peaks: 307 WARNING @ Sun, 02 Jun 2019 21:47:01: Fewer paired peaks (307) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 307 pairs to build model! INFO @ Sun, 02 Jun 2019 21:47:01: start model_add_line... INFO @ Sun, 02 Jun 2019 21:47:01: start X-correlation... INFO @ Sun, 02 Jun 2019 21:47:01: end of X-cor INFO @ Sun, 02 Jun 2019 21:47:01: #2 finished! INFO @ Sun, 02 Jun 2019 21:47:01: #2 predicted fragment length is 48 bps INFO @ Sun, 02 Jun 2019 21:47:01: #2 alternative fragment length(s) may be 2,48,578 bps INFO @ Sun, 02 Jun 2019 21:47:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020828/SRX5020828.05_model.r WARNING @ Sun, 02 Jun 2019 21:47:01: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:47:01: #2 You may need to consider one of the other alternative d(s): 2,48,578 WARNING @ Sun, 02 Jun 2019 21:47:01: #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 21:47:01: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:47:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:47:05: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:47:05: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:47:05: #1 total tags in treatment: 11772080 INFO @ Sun, 02 Jun 2019 21:47:05: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:47:05: #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 21:47:05: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:47:05: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:47:05: #1 total tags in treatment: 11772080 INFO @ Sun, 02 Jun 2019 21:47:05: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:47:05: #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 21:47:05: #1 tags after filtering in treatment: 11772080 INFO @ Sun, 02 Jun 2019 21:47:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:47:05: #1 finished! INFO @ Sun, 02 Jun 2019 21:47:05: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:47:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:47:06: #1 tags after filtering in treatment: 11772080 INFO @ Sun, 02 Jun 2019 21:47:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:47:06: #1 finished! INFO @ Sun, 02 Jun 2019 21:47:06: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:47:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:47:07: #2 number of paired peaks: 307 WARNING @ Sun, 02 Jun 2019 21:47:07: Fewer paired peaks (307) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 307 pairs to build model! INFO @ Sun, 02 Jun 2019 21:47:07: start model_add_line... INFO @ Sun, 02 Jun 2019 21:47:07: #2 number of paired peaks: 307 WARNING @ Sun, 02 Jun 2019 21:47:07: Fewer paired peaks (307) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 307 pairs to build model! INFO @ Sun, 02 Jun 2019 21:47:07: start model_add_line... INFO @ Sun, 02 Jun 2019 21:47:07: start X-correlation... INFO @ Sun, 02 Jun 2019 21:47:07: end of X-cor INFO @ Sun, 02 Jun 2019 21:47:07: #2 finished! INFO @ Sun, 02 Jun 2019 21:47:07: #2 predicted fragment length is 48 bps INFO @ Sun, 02 Jun 2019 21:47:07: #2 alternative fragment length(s) may be 2,48,578 bps INFO @ Sun, 02 Jun 2019 21:47:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020828/SRX5020828.20_model.r WARNING @ Sun, 02 Jun 2019 21:47:07: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:47:07: #2 You may need to consider one of the other alternative d(s): 2,48,578 WARNING @ Sun, 02 Jun 2019 21:47:07: #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 21:47:07: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:47:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:47:07: start X-correlation... INFO @ Sun, 02 Jun 2019 21:47:07: end of X-cor INFO @ Sun, 02 Jun 2019 21:47:07: #2 finished! INFO @ Sun, 02 Jun 2019 21:47:07: #2 predicted fragment length is 48 bps INFO @ Sun, 02 Jun 2019 21:47:07: #2 alternative fragment length(s) may be 2,48,578 bps INFO @ Sun, 02 Jun 2019 21:47:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020828/SRX5020828.10_model.r WARNING @ Sun, 02 Jun 2019 21:47:07: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:47:07: #2 You may need to consider one of the other alternative d(s): 2,48,578 WARNING @ Sun, 02 Jun 2019 21:47:07: #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 21:47:07: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:47:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:47:33: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:47:37: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:47:38: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:47:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020828/SRX5020828.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:47:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020828/SRX5020828.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:47:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020828/SRX5020828.05_summits.bed INFO @ Sun, 02 Jun 2019 21:47:48: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (666 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:47:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020828/SRX5020828.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:47:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020828/SRX5020828.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:47:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020828/SRX5020828.10_summits.bed INFO @ Sun, 02 Jun 2019 21:47:53: Done! INFO @ Sun, 02 Jun 2019 21:47:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020828/SRX5020828.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:47:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020828/SRX5020828.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:47:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020828/SRX5020828.20_summits.bed INFO @ Sun, 02 Jun 2019 21:47:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (429 records, 4 fields): 3 millis pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (172 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。