Job ID = 1294244 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,810,536 reads read : 21,810,536 reads written : 21,810,536 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: 00:10:38 21810536 reads; of these: 21810536 (100.00%) were unpaired; of these: 6126926 (28.09%) aligned 0 times 10655730 (48.86%) aligned exactly 1 time 5027880 (23.05%) aligned >1 times 71.91% overall alignment rate Time searching: 00:10:38 Overall time: 00:10:38 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] 4203599 / 15683610 = 0.2680 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 06:08:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX203001/SRX203001.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX203001/SRX203001.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX203001/SRX203001.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX203001/SRX203001.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 06:08:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:08:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX203001/SRX203001.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX203001/SRX203001.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX203001/SRX203001.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX203001/SRX203001.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 06:08:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:08:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:08:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:08:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX203001/SRX203001.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX203001/SRX203001.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX203001/SRX203001.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX203001/SRX203001.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 06:08:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:08:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:08:40: 1000000 INFO @ Mon, 03 Jun 2019 06:08:40: 1000000 INFO @ Mon, 03 Jun 2019 06:08:42: 1000000 INFO @ Mon, 03 Jun 2019 06:08:47: 2000000 INFO @ Mon, 03 Jun 2019 06:08:48: 2000000 INFO @ Mon, 03 Jun 2019 06:08:51: 2000000 INFO @ Mon, 03 Jun 2019 06:08:54: 3000000 INFO @ Mon, 03 Jun 2019 06:08:56: 3000000 INFO @ Mon, 03 Jun 2019 06:08:59: 3000000 INFO @ Mon, 03 Jun 2019 06:09:01: 4000000 INFO @ Mon, 03 Jun 2019 06:09:03: 4000000 INFO @ Mon, 03 Jun 2019 06:09:08: 5000000 INFO @ Mon, 03 Jun 2019 06:09:08: 4000000 INFO @ Mon, 03 Jun 2019 06:09:11: 5000000 INFO @ Mon, 03 Jun 2019 06:09:15: 6000000 INFO @ Mon, 03 Jun 2019 06:09:17: 5000000 INFO @ Mon, 03 Jun 2019 06:09:18: 6000000 INFO @ Mon, 03 Jun 2019 06:09:22: 7000000 INFO @ Mon, 03 Jun 2019 06:09:25: 6000000 INFO @ Mon, 03 Jun 2019 06:09:25: 7000000 INFO @ Mon, 03 Jun 2019 06:09:29: 8000000 INFO @ Mon, 03 Jun 2019 06:09:33: 8000000 INFO @ Mon, 03 Jun 2019 06:09:34: 7000000 INFO @ Mon, 03 Jun 2019 06:09:36: 9000000 INFO @ Mon, 03 Jun 2019 06:09:41: 9000000 INFO @ Mon, 03 Jun 2019 06:09:42: 8000000 INFO @ Mon, 03 Jun 2019 06:09:44: 10000000 INFO @ Mon, 03 Jun 2019 06:09:49: 10000000 INFO @ Mon, 03 Jun 2019 06:09:51: 11000000 INFO @ Mon, 03 Jun 2019 06:09:51: 9000000 INFO @ Mon, 03 Jun 2019 06:09:54: #1 tag size is determined as 54 bps INFO @ Mon, 03 Jun 2019 06:09:54: #1 tag size = 54 INFO @ Mon, 03 Jun 2019 06:09:54: #1 total tags in treatment: 11480011 INFO @ Mon, 03 Jun 2019 06:09:54: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:09:54: #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 06:09:55: #1 tags after filtering in treatment: 11480011 INFO @ Mon, 03 Jun 2019 06:09:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:09:55: #1 finished! INFO @ Mon, 03 Jun 2019 06:09:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:09:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:09:56: #2 number of paired peaks: 414 WARNING @ Mon, 03 Jun 2019 06:09:56: Fewer paired peaks (414) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 414 pairs to build model! INFO @ Mon, 03 Jun 2019 06:09:56: start model_add_line... INFO @ Mon, 03 Jun 2019 06:09:56: start X-correlation... INFO @ Mon, 03 Jun 2019 06:09:56: end of X-cor INFO @ Mon, 03 Jun 2019 06:09:56: #2 finished! INFO @ Mon, 03 Jun 2019 06:09:56: #2 predicted fragment length is 41 bps INFO @ Mon, 03 Jun 2019 06:09:56: #2 alternative fragment length(s) may be 3,41,524,562 bps INFO @ Mon, 03 Jun 2019 06:09:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX203001/SRX203001.20_model.r WARNING @ Mon, 03 Jun 2019 06:09:56: #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 06:09:56: #2 You may need to consider one of the other alternative d(s): 3,41,524,562 WARNING @ Mon, 03 Jun 2019 06:09:56: #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 06:09:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:09:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:09:56: 11000000 INFO @ Mon, 03 Jun 2019 06:10:00: 10000000 INFO @ Mon, 03 Jun 2019 06:10:00: #1 tag size is determined as 54 bps INFO @ Mon, 03 Jun 2019 06:10:00: #1 tag size = 54 INFO @ Mon, 03 Jun 2019 06:10:00: #1 total tags in treatment: 11480011 INFO @ Mon, 03 Jun 2019 06:10:00: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:10:00: #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 06:10:00: #1 tags after filtering in treatment: 11480011 INFO @ Mon, 03 Jun 2019 06:10:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:10:00: #1 finished! INFO @ Mon, 03 Jun 2019 06:10:00: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:10:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:10:02: #2 number of paired peaks: 414 WARNING @ Mon, 03 Jun 2019 06:10:02: Fewer paired peaks (414) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 414 pairs to build model! INFO @ Mon, 03 Jun 2019 06:10:02: start model_add_line... INFO @ Mon, 03 Jun 2019 06:10:02: start X-correlation... INFO @ Mon, 03 Jun 2019 06:10:02: end of X-cor INFO @ Mon, 03 Jun 2019 06:10:02: #2 finished! INFO @ Mon, 03 Jun 2019 06:10:02: #2 predicted fragment length is 41 bps INFO @ Mon, 03 Jun 2019 06:10:02: #2 alternative fragment length(s) may be 3,41,524,562 bps INFO @ Mon, 03 Jun 2019 06:10:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX203001/SRX203001.10_model.r WARNING @ Mon, 03 Jun 2019 06:10:02: #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 06:10:02: #2 You may need to consider one of the other alternative d(s): 3,41,524,562 WARNING @ Mon, 03 Jun 2019 06:10:02: #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 06:10:02: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:10:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:10:08: 11000000 INFO @ Mon, 03 Jun 2019 06:10:13: #1 tag size is determined as 54 bps INFO @ Mon, 03 Jun 2019 06:10:13: #1 tag size = 54 INFO @ Mon, 03 Jun 2019 06:10:13: #1 total tags in treatment: 11480011 INFO @ Mon, 03 Jun 2019 06:10:13: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:10:13: #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 06:10:13: #1 tags after filtering in treatment: 11480011 INFO @ Mon, 03 Jun 2019 06:10:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:10:13: #1 finished! INFO @ Mon, 03 Jun 2019 06:10:13: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:10:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:10:14: #2 number of paired peaks: 414 WARNING @ Mon, 03 Jun 2019 06:10:14: Fewer paired peaks (414) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 414 pairs to build model! INFO @ Mon, 03 Jun 2019 06:10:14: start model_add_line... INFO @ Mon, 03 Jun 2019 06:10:14: start X-correlation... INFO @ Mon, 03 Jun 2019 06:10:14: end of X-cor INFO @ Mon, 03 Jun 2019 06:10:14: #2 finished! INFO @ Mon, 03 Jun 2019 06:10:14: #2 predicted fragment length is 41 bps INFO @ Mon, 03 Jun 2019 06:10:14: #2 alternative fragment length(s) may be 3,41,524,562 bps INFO @ Mon, 03 Jun 2019 06:10:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX203001/SRX203001.05_model.r WARNING @ Mon, 03 Jun 2019 06:10:14: #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 06:10:14: #2 You may need to consider one of the other alternative d(s): 3,41,524,562 WARNING @ Mon, 03 Jun 2019 06:10:14: #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 06:10:14: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:10:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:10:28: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:10:34: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:10:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX203001/SRX203001.20_peaks.xls INFO @ Mon, 03 Jun 2019 06:10:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX203001/SRX203001.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:10:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX203001/SRX203001.20_summits.bed INFO @ Mon, 03 Jun 2019 06:10:44: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (687 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:10:46: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:10:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX203001/SRX203001.10_peaks.xls INFO @ Mon, 03 Jun 2019 06:10:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX203001/SRX203001.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:10:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX203001/SRX203001.10_summits.bed INFO @ Mon, 03 Jun 2019 06:10:50: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1433 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:11:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX203001/SRX203001.05_peaks.xls INFO @ Mon, 03 Jun 2019 06:11:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX203001/SRX203001.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:11:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX203001/SRX203001.05_summits.bed INFO @ Mon, 03 Jun 2019 06:11:02: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2696 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。