Job ID = 1294669 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,667,108 reads read : 17,667,108 reads written : 17,667,108 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: 00:09:15 17667108 reads; of these: 17667108 (100.00%) were unpaired; of these: 720178 (4.08%) aligned 0 times 11489754 (65.03%) aligned exactly 1 time 5457176 (30.89%) aligned >1 times 95.92% overall alignment rate Time searching: 00:09:15 Overall time: 00:09:15 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1984270 / 16946930 = 0.1171 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 @ Mon, 03 Jun 2019 09:53:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287814/SRX287814.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287814/SRX287814.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287814/SRX287814.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287814/SRX287814.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 09:53:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:53:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:53:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287814/SRX287814.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287814/SRX287814.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287814/SRX287814.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287814/SRX287814.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 09:53:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:53:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:53:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287814/SRX287814.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287814/SRX287814.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287814/SRX287814.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287814/SRX287814.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 09:53:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:53:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:53:48: 1000000 INFO @ Mon, 03 Jun 2019 09:53:48: 1000000 INFO @ Mon, 03 Jun 2019 09:53:49: 1000000 INFO @ Mon, 03 Jun 2019 09:53:56: 2000000 INFO @ Mon, 03 Jun 2019 09:53:56: 2000000 INFO @ Mon, 03 Jun 2019 09:53:57: 2000000 INFO @ Mon, 03 Jun 2019 09:54:03: 3000000 INFO @ Mon, 03 Jun 2019 09:54:03: 3000000 INFO @ Mon, 03 Jun 2019 09:54:06: 3000000 INFO @ Mon, 03 Jun 2019 09:54:11: 4000000 INFO @ Mon, 03 Jun 2019 09:54:11: 4000000 INFO @ Mon, 03 Jun 2019 09:54:14: 4000000 INFO @ Mon, 03 Jun 2019 09:54:18: 5000000 INFO @ Mon, 03 Jun 2019 09:54:19: 5000000 INFO @ Mon, 03 Jun 2019 09:54:23: 5000000 INFO @ Mon, 03 Jun 2019 09:54:25: 6000000 INFO @ Mon, 03 Jun 2019 09:54:26: 6000000 INFO @ Mon, 03 Jun 2019 09:54:31: 6000000 INFO @ Mon, 03 Jun 2019 09:54:33: 7000000 INFO @ Mon, 03 Jun 2019 09:54:34: 7000000 INFO @ Mon, 03 Jun 2019 09:54:40: 7000000 INFO @ Mon, 03 Jun 2019 09:54:40: 8000000 INFO @ Mon, 03 Jun 2019 09:54:41: 8000000 INFO @ Mon, 03 Jun 2019 09:54:47: 9000000 INFO @ Mon, 03 Jun 2019 09:54:48: 8000000 INFO @ Mon, 03 Jun 2019 09:54:48: 9000000 INFO @ Mon, 03 Jun 2019 09:54:55: 10000000 INFO @ Mon, 03 Jun 2019 09:54:56: 10000000 INFO @ Mon, 03 Jun 2019 09:54:57: 9000000 INFO @ Mon, 03 Jun 2019 09:55:02: 11000000 INFO @ Mon, 03 Jun 2019 09:55:03: 11000000 INFO @ Mon, 03 Jun 2019 09:55:05: 10000000 INFO @ Mon, 03 Jun 2019 09:55:09: 12000000 INFO @ Mon, 03 Jun 2019 09:55:10: 12000000 INFO @ Mon, 03 Jun 2019 09:55:13: 11000000 INFO @ Mon, 03 Jun 2019 09:55:16: 13000000 INFO @ Mon, 03 Jun 2019 09:55:17: 13000000 INFO @ Mon, 03 Jun 2019 09:55:22: 12000000 INFO @ Mon, 03 Jun 2019 09:55:24: 14000000 INFO @ Mon, 03 Jun 2019 09:55:24: 14000000 INFO @ Mon, 03 Jun 2019 09:55:30: 13000000 INFO @ Mon, 03 Jun 2019 09:55:31: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:55:31: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:55:31: #1 total tags in treatment: 14962660 INFO @ Mon, 03 Jun 2019 09:55:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:55:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 09:55:31: #1 tags after filtering in treatment: 14962660 INFO @ Mon, 03 Jun 2019 09:55:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:55:31: #1 finished! INFO @ Mon, 03 Jun 2019 09:55:31: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:55:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:55:32: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:55:32: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:55:32: #1 total tags in treatment: 14962660 INFO @ Mon, 03 Jun 2019 09:55:32: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:55:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 09:55:32: #1 tags after filtering in treatment: 14962660 INFO @ Mon, 03 Jun 2019 09:55:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:55:32: #1 finished! INFO @ Mon, 03 Jun 2019 09:55:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:55:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:55:32: #2 number of paired peaks: 298 WARNING @ Mon, 03 Jun 2019 09:55:32: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Mon, 03 Jun 2019 09:55:32: start model_add_line... INFO @ Mon, 03 Jun 2019 09:55:33: start X-correlation... INFO @ Mon, 03 Jun 2019 09:55:33: end of X-cor INFO @ Mon, 03 Jun 2019 09:55:33: #2 finished! INFO @ Mon, 03 Jun 2019 09:55:33: #2 predicted fragment length is 41 bps INFO @ Mon, 03 Jun 2019 09:55:33: #2 alternative fragment length(s) may be 41 bps INFO @ Mon, 03 Jun 2019 09:55:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287814/SRX287814.05_model.r WARNING @ Mon, 03 Jun 2019 09:55:33: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:55:33: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Mon, 03 Jun 2019 09:55:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 09:55:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:55:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:55:34: #2 number of paired peaks: 298 WARNING @ Mon, 03 Jun 2019 09:55:34: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Mon, 03 Jun 2019 09:55:34: start model_add_line... INFO @ Mon, 03 Jun 2019 09:55:34: start X-correlation... INFO @ Mon, 03 Jun 2019 09:55:34: end of X-cor INFO @ Mon, 03 Jun 2019 09:55:34: #2 finished! INFO @ Mon, 03 Jun 2019 09:55:34: #2 predicted fragment length is 41 bps INFO @ Mon, 03 Jun 2019 09:55:34: #2 alternative fragment length(s) may be 41 bps INFO @ Mon, 03 Jun 2019 09:55:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287814/SRX287814.20_model.r WARNING @ Mon, 03 Jun 2019 09:55:34: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:55:34: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Mon, 03 Jun 2019 09:55:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 09:55:34: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:55:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:55:39: 14000000 INFO @ Mon, 03 Jun 2019 09:55:47: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:55:47: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:55:47: #1 total tags in treatment: 14962660 INFO @ Mon, 03 Jun 2019 09:55:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:55:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 09:55:47: #1 tags after filtering in treatment: 14962660 INFO @ Mon, 03 Jun 2019 09:55:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:55:47: #1 finished! INFO @ Mon, 03 Jun 2019 09:55:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:55:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:55:48: #2 number of paired peaks: 298 WARNING @ Mon, 03 Jun 2019 09:55:48: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Mon, 03 Jun 2019 09:55:48: start model_add_line... INFO @ Mon, 03 Jun 2019 09:55:49: start X-correlation... INFO @ Mon, 03 Jun 2019 09:55:49: end of X-cor INFO @ Mon, 03 Jun 2019 09:55:49: #2 finished! INFO @ Mon, 03 Jun 2019 09:55:49: #2 predicted fragment length is 41 bps INFO @ Mon, 03 Jun 2019 09:55:49: #2 alternative fragment length(s) may be 41 bps INFO @ Mon, 03 Jun 2019 09:55:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287814/SRX287814.10_model.r WARNING @ Mon, 03 Jun 2019 09:55:49: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:55:49: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Mon, 03 Jun 2019 09:55:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 09:55:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:55:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:56:12: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:56:13: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:56:28: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:56:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287814/SRX287814.05_peaks.xls INFO @ Mon, 03 Jun 2019 09:56:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287814/SRX287814.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:56:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287814/SRX287814.05_summits.bed INFO @ Mon, 03 Jun 2019 09:56:31: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2147 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:56:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287814/SRX287814.20_peaks.xls INFO @ Mon, 03 Jun 2019 09:56:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287814/SRX287814.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:56:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287814/SRX287814.20_summits.bed INFO @ Mon, 03 Jun 2019 09:56:33: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1458 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:56:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287814/SRX287814.10_peaks.xls INFO @ Mon, 03 Jun 2019 09:56:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287814/SRX287814.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:56:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287814/SRX287814.10_summits.bed INFO @ Mon, 03 Jun 2019 09:56:47: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1884 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。