Job ID = 1293085 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,812,743 reads read : 18,812,743 reads written : 18,812,743 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: 00:05:12 18812743 reads; of these: 18812743 (100.00%) were unpaired; of these: 150188 (0.80%) aligned 0 times 15590706 (82.87%) aligned exactly 1 time 3071849 (16.33%) aligned >1 times 99.20% overall alignment rate Time searching: 00:05:12 Overall time: 00:05:12 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] 8432998 / 18662555 = 0.4519 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 21:53:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020845/SRX5020845.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020845/SRX5020845.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020845/SRX5020845.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020845/SRX5020845.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 21:53:37: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:53:37: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:53:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020845/SRX5020845.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020845/SRX5020845.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020845/SRX5020845.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020845/SRX5020845.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 21:53:38: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:53:38: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:53:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020845/SRX5020845.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020845/SRX5020845.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020845/SRX5020845.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020845/SRX5020845.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 21:53:38: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:53:38: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:53:45: 1000000 INFO @ Sun, 02 Jun 2019 21:53:45: 1000000 INFO @ Sun, 02 Jun 2019 21:53:47: 1000000 INFO @ Sun, 02 Jun 2019 21:53:52: 2000000 INFO @ Sun, 02 Jun 2019 21:53:52: 2000000 INFO @ Sun, 02 Jun 2019 21:53:56: 2000000 INFO @ Sun, 02 Jun 2019 21:53:59: 3000000 INFO @ Sun, 02 Jun 2019 21:53:59: 3000000 INFO @ Sun, 02 Jun 2019 21:54:05: 3000000 INFO @ Sun, 02 Jun 2019 21:54:06: 4000000 INFO @ Sun, 02 Jun 2019 21:54:06: 4000000 INFO @ Sun, 02 Jun 2019 21:54:13: 5000000 INFO @ Sun, 02 Jun 2019 21:54:13: 5000000 INFO @ Sun, 02 Jun 2019 21:54:13: 4000000 INFO @ Sun, 02 Jun 2019 21:54:20: 6000000 INFO @ Sun, 02 Jun 2019 21:54:20: 6000000 INFO @ Sun, 02 Jun 2019 21:54:22: 5000000 INFO @ Sun, 02 Jun 2019 21:54:27: 7000000 INFO @ Sun, 02 Jun 2019 21:54:27: 7000000 INFO @ Sun, 02 Jun 2019 21:54:31: 6000000 INFO @ Sun, 02 Jun 2019 21:54:33: 8000000 INFO @ Sun, 02 Jun 2019 21:54:34: 8000000 INFO @ Sun, 02 Jun 2019 21:54:39: 7000000 INFO @ Sun, 02 Jun 2019 21:54:40: 9000000 INFO @ Sun, 02 Jun 2019 21:54:41: 9000000 INFO @ Sun, 02 Jun 2019 21:54:47: 10000000 INFO @ Sun, 02 Jun 2019 21:54:48: 10000000 INFO @ Sun, 02 Jun 2019 21:54:48: 8000000 INFO @ Sun, 02 Jun 2019 21:54:49: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 21:54:49: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 21:54:49: #1 total tags in treatment: 10229557 INFO @ Sun, 02 Jun 2019 21:54:49: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:54:49: #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 21:54:49: #1 tags after filtering in treatment: 10229557 INFO @ Sun, 02 Jun 2019 21:54:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:54:49: #1 finished! INFO @ Sun, 02 Jun 2019 21:54:49: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:54:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:54:50: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 21:54:50: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 21:54:50: #1 total tags in treatment: 10229557 INFO @ Sun, 02 Jun 2019 21:54:50: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:54:50: #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 21:54:50: #1 tags after filtering in treatment: 10229557 INFO @ Sun, 02 Jun 2019 21:54:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:54:50: #1 finished! INFO @ Sun, 02 Jun 2019 21:54:50: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:54:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:54:50: #2 number of paired peaks: 434 WARNING @ Sun, 02 Jun 2019 21:54:50: Fewer paired peaks (434) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 434 pairs to build model! INFO @ Sun, 02 Jun 2019 21:54:50: start model_add_line... INFO @ Sun, 02 Jun 2019 21:54:50: start X-correlation... INFO @ Sun, 02 Jun 2019 21:54:50: end of X-cor INFO @ Sun, 02 Jun 2019 21:54:50: #2 finished! INFO @ Sun, 02 Jun 2019 21:54:50: #2 predicted fragment length is 47 bps INFO @ Sun, 02 Jun 2019 21:54:50: #2 alternative fragment length(s) may be 2,47 bps INFO @ Sun, 02 Jun 2019 21:54:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020845/SRX5020845.20_model.r WARNING @ Sun, 02 Jun 2019 21:54:50: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:54:50: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Sun, 02 Jun 2019 21:54:50: #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 21:54:50: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:54:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:54:51: #2 number of paired peaks: 434 WARNING @ Sun, 02 Jun 2019 21:54:51: Fewer paired peaks (434) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 434 pairs to build model! INFO @ Sun, 02 Jun 2019 21:54:51: start model_add_line... INFO @ Sun, 02 Jun 2019 21:54:51: start X-correlation... INFO @ Sun, 02 Jun 2019 21:54:51: end of X-cor INFO @ Sun, 02 Jun 2019 21:54:51: #2 finished! INFO @ Sun, 02 Jun 2019 21:54:51: #2 predicted fragment length is 47 bps INFO @ Sun, 02 Jun 2019 21:54:51: #2 alternative fragment length(s) may be 2,47 bps INFO @ Sun, 02 Jun 2019 21:54:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020845/SRX5020845.10_model.r WARNING @ Sun, 02 Jun 2019 21:54:51: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:54:51: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Sun, 02 Jun 2019 21:54:51: #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 21:54:51: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:54:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:54:57: 9000000 INFO @ Sun, 02 Jun 2019 21:55:05: 10000000 INFO @ Sun, 02 Jun 2019 21:55:07: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 21:55:07: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 21:55:07: #1 total tags in treatment: 10229557 INFO @ Sun, 02 Jun 2019 21:55:07: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:55:07: #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 21:55:07: #1 tags after filtering in treatment: 10229557 INFO @ Sun, 02 Jun 2019 21:55:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:55:07: #1 finished! INFO @ Sun, 02 Jun 2019 21:55:07: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:55:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:55:08: #2 number of paired peaks: 434 WARNING @ Sun, 02 Jun 2019 21:55:08: Fewer paired peaks (434) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 434 pairs to build model! INFO @ Sun, 02 Jun 2019 21:55:08: start model_add_line... INFO @ Sun, 02 Jun 2019 21:55:08: start X-correlation... INFO @ Sun, 02 Jun 2019 21:55:08: end of X-cor INFO @ Sun, 02 Jun 2019 21:55:08: #2 finished! INFO @ Sun, 02 Jun 2019 21:55:08: #2 predicted fragment length is 47 bps INFO @ Sun, 02 Jun 2019 21:55:08: #2 alternative fragment length(s) may be 2,47 bps INFO @ Sun, 02 Jun 2019 21:55:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020845/SRX5020845.05_model.r WARNING @ Sun, 02 Jun 2019 21:55:08: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:55:08: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Sun, 02 Jun 2019 21:55:08: #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 21:55:08: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:55:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:55:17: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:55:18: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:55:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020845/SRX5020845.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:55:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020845/SRX5020845.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:55:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020845/SRX5020845.20_summits.bed INFO @ Sun, 02 Jun 2019 21:55:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (215 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:55:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020845/SRX5020845.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:55:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020845/SRX5020845.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:55:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020845/SRX5020845.10_summits.bed INFO @ Sun, 02 Jun 2019 21:55:32: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (567 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:55:36: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:55:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020845/SRX5020845.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:55:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020845/SRX5020845.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:55:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020845/SRX5020845.05_summits.bed INFO @ Sun, 02 Jun 2019 21:55:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (752 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。