Job ID = 2590870 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,897,755 reads read : 15,795,510 reads written : 7,897,755 reads 0-length : 7,897,755 rm: cannot remove ‘[DSE]RR*’: 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: 00:03:40 7897755 reads; of these: 7897755 (100.00%) were unpaired; of these: 689098 (8.73%) aligned 0 times 5274698 (66.79%) aligned exactly 1 time 1933959 (24.49%) aligned >1 times 91.27% overall alignment rate Time searching: 00:03:40 Overall time: 00:03:40 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_rmdupse_core] 1507745 / 7208657 = 0.2092 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, 12 Aug 2019 23:53:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5053153/SRX5053153.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5053153/SRX5053153.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5053153/SRX5053153.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5053153/SRX5053153.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, 12 Aug 2019 23:53:17: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:53:17: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:53:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5053153/SRX5053153.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5053153/SRX5053153.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5053153/SRX5053153.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5053153/SRX5053153.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, 12 Aug 2019 23:53:18: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:53:18: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:53:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5053153/SRX5053153.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5053153/SRX5053153.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5053153/SRX5053153.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5053153/SRX5053153.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, 12 Aug 2019 23:53:19: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:53:19: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:53:27: 1000000 INFO @ Mon, 12 Aug 2019 23:53:29: 1000000 INFO @ Mon, 12 Aug 2019 23:53:31: 1000000 INFO @ Mon, 12 Aug 2019 23:53:37: 2000000 INFO @ Mon, 12 Aug 2019 23:53:40: 2000000 INFO @ Mon, 12 Aug 2019 23:53:43: 2000000 INFO @ Mon, 12 Aug 2019 23:53:46: 3000000 INFO @ Mon, 12 Aug 2019 23:53:50: 3000000 INFO @ Mon, 12 Aug 2019 23:53:55: 3000000 INFO @ Mon, 12 Aug 2019 23:53:56: 4000000 INFO @ Mon, 12 Aug 2019 23:54:01: 4000000 INFO @ Mon, 12 Aug 2019 23:54:06: 5000000 INFO @ Mon, 12 Aug 2019 23:54:06: 4000000 INFO @ Mon, 12 Aug 2019 23:54:12: 5000000 INFO @ Mon, 12 Aug 2019 23:54:13: #1 tag size is determined as 75 bps INFO @ Mon, 12 Aug 2019 23:54:13: #1 tag size = 75 INFO @ Mon, 12 Aug 2019 23:54:13: #1 total tags in treatment: 5700912 INFO @ Mon, 12 Aug 2019 23:54:13: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:54:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:54:13: #1 tags after filtering in treatment: 5700912 INFO @ Mon, 12 Aug 2019 23:54:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:54:13: #1 finished! INFO @ Mon, 12 Aug 2019 23:54:13: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:54:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:54:13: #2 number of paired peaks: 1235 INFO @ Mon, 12 Aug 2019 23:54:13: start model_add_line... INFO @ Mon, 12 Aug 2019 23:54:14: start X-correlation... INFO @ Mon, 12 Aug 2019 23:54:14: end of X-cor INFO @ Mon, 12 Aug 2019 23:54:14: #2 finished! INFO @ Mon, 12 Aug 2019 23:54:14: #2 predicted fragment length is 80 bps INFO @ Mon, 12 Aug 2019 23:54:14: #2 alternative fragment length(s) may be 80 bps INFO @ Mon, 12 Aug 2019 23:54:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5053153/SRX5053153.05_model.r WARNING @ Mon, 12 Aug 2019 23:54:14: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:54:14: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Mon, 12 Aug 2019 23:54:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:54:14: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:54:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:54:18: 5000000 INFO @ Mon, 12 Aug 2019 23:54:19: #1 tag size is determined as 75 bps INFO @ Mon, 12 Aug 2019 23:54:19: #1 tag size = 75 INFO @ Mon, 12 Aug 2019 23:54:19: #1 total tags in treatment: 5700912 INFO @ Mon, 12 Aug 2019 23:54:19: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:54:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:54:19: #1 tags after filtering in treatment: 5700912 INFO @ Mon, 12 Aug 2019 23:54:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:54:19: #1 finished! INFO @ Mon, 12 Aug 2019 23:54:19: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:54:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:54:20: #2 number of paired peaks: 1235 INFO @ Mon, 12 Aug 2019 23:54:20: start model_add_line... INFO @ Mon, 12 Aug 2019 23:54:20: start X-correlation... INFO @ Mon, 12 Aug 2019 23:54:20: end of X-cor INFO @ Mon, 12 Aug 2019 23:54:20: #2 finished! INFO @ Mon, 12 Aug 2019 23:54:20: #2 predicted fragment length is 80 bps INFO @ Mon, 12 Aug 2019 23:54:20: #2 alternative fragment length(s) may be 80 bps INFO @ Mon, 12 Aug 2019 23:54:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5053153/SRX5053153.10_model.r WARNING @ Mon, 12 Aug 2019 23:54:20: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:54:20: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Mon, 12 Aug 2019 23:54:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:54:20: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:54:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:54:26: #1 tag size is determined as 75 bps INFO @ Mon, 12 Aug 2019 23:54:26: #1 tag size = 75 INFO @ Mon, 12 Aug 2019 23:54:26: #1 total tags in treatment: 5700912 INFO @ Mon, 12 Aug 2019 23:54:26: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:54:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:54:26: #1 tags after filtering in treatment: 5700912 INFO @ Mon, 12 Aug 2019 23:54:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:54:26: #1 finished! INFO @ Mon, 12 Aug 2019 23:54:26: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:54:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:54:27: #2 number of paired peaks: 1235 INFO @ Mon, 12 Aug 2019 23:54:27: start model_add_line... INFO @ Mon, 12 Aug 2019 23:54:27: start X-correlation... INFO @ Mon, 12 Aug 2019 23:54:27: end of X-cor INFO @ Mon, 12 Aug 2019 23:54:27: #2 finished! INFO @ Mon, 12 Aug 2019 23:54:27: #2 predicted fragment length is 80 bps INFO @ Mon, 12 Aug 2019 23:54:27: #2 alternative fragment length(s) may be 80 bps INFO @ Mon, 12 Aug 2019 23:54:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5053153/SRX5053153.20_model.r WARNING @ Mon, 12 Aug 2019 23:54:27: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:54:27: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Mon, 12 Aug 2019 23:54:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:54:27: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:54:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:54:31: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:54:38: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:54:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5053153/SRX5053153.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:54:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5053153/SRX5053153.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:54:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5053153/SRX5053153.05_summits.bed INFO @ Mon, 12 Aug 2019 23:54:40: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2044 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:54:44: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:54:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5053153/SRX5053153.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:54:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5053153/SRX5053153.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:54:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5053153/SRX5053153.10_summits.bed INFO @ Mon, 12 Aug 2019 23:54:47: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1057 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:54:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5053153/SRX5053153.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:54:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5053153/SRX5053153.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:54:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5053153/SRX5053153.20_summits.bed INFO @ Mon, 12 Aug 2019 23:54:53: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (563 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。