Job ID = 1294107 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 31,079,613 reads read : 31,079,613 reads written : 31,079,613 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: 00:10:01 31079613 reads; of these: 31079613 (100.00%) were unpaired; of these: 1717638 (5.53%) aligned 0 times 23663956 (76.14%) aligned exactly 1 time 5698019 (18.33%) aligned >1 times 94.47% overall alignment rate Time searching: 00:10:01 Overall time: 00:10:01 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 12 files... [bam_rmdupse_core] 20074141 / 29361975 = 0.6837 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 05:24:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX186112/SRX186112.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX186112/SRX186112.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX186112/SRX186112.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX186112/SRX186112.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 05:24:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:24:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:24:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX186112/SRX186112.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX186112/SRX186112.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX186112/SRX186112.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX186112/SRX186112.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 05:24:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:24:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:24:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX186112/SRX186112.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX186112/SRX186112.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX186112/SRX186112.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX186112/SRX186112.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 05:24:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:24:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:24:29: 1000000 INFO @ Mon, 03 Jun 2019 05:24:30: 1000000 INFO @ Mon, 03 Jun 2019 05:24:31: 1000000 INFO @ Mon, 03 Jun 2019 05:24:38: 2000000 INFO @ Mon, 03 Jun 2019 05:24:39: 2000000 INFO @ Mon, 03 Jun 2019 05:24:41: 2000000 INFO @ Mon, 03 Jun 2019 05:24:47: 3000000 INFO @ Mon, 03 Jun 2019 05:24:47: 3000000 INFO @ Mon, 03 Jun 2019 05:24:51: 3000000 INFO @ Mon, 03 Jun 2019 05:24:56: 4000000 INFO @ Mon, 03 Jun 2019 05:24:56: 4000000 INFO @ Mon, 03 Jun 2019 05:25:01: 4000000 INFO @ Mon, 03 Jun 2019 05:25:04: 5000000 INFO @ Mon, 03 Jun 2019 05:25:05: 5000000 INFO @ Mon, 03 Jun 2019 05:25:10: 5000000 INFO @ Mon, 03 Jun 2019 05:25:13: 6000000 INFO @ Mon, 03 Jun 2019 05:25:13: 6000000 INFO @ Mon, 03 Jun 2019 05:25:20: 6000000 INFO @ Mon, 03 Jun 2019 05:25:22: 7000000 INFO @ Mon, 03 Jun 2019 05:25:22: 7000000 INFO @ Mon, 03 Jun 2019 05:25:30: 7000000 INFO @ Mon, 03 Jun 2019 05:25:31: 8000000 INFO @ Mon, 03 Jun 2019 05:25:31: 8000000 INFO @ Mon, 03 Jun 2019 05:25:39: 9000000 INFO @ Mon, 03 Jun 2019 05:25:40: 8000000 INFO @ Mon, 03 Jun 2019 05:25:40: 9000000 INFO @ Mon, 03 Jun 2019 05:25:42: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 05:25:42: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 05:25:42: #1 total tags in treatment: 9287834 INFO @ Mon, 03 Jun 2019 05:25:42: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:25:42: #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 05:25:42: #1 tags after filtering in treatment: 9287834 INFO @ Mon, 03 Jun 2019 05:25:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:25:42: #1 finished! INFO @ Mon, 03 Jun 2019 05:25:42: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:25:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:25:42: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 05:25:42: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 05:25:42: #1 total tags in treatment: 9287834 INFO @ Mon, 03 Jun 2019 05:25:42: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:25:42: #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 05:25:43: #1 tags after filtering in treatment: 9287834 INFO @ Mon, 03 Jun 2019 05:25:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:25:43: #1 finished! INFO @ Mon, 03 Jun 2019 05:25:43: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:25:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:25:43: #2 number of paired peaks: 756 WARNING @ Mon, 03 Jun 2019 05:25:43: Fewer paired peaks (756) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 756 pairs to build model! INFO @ Mon, 03 Jun 2019 05:25:43: start model_add_line... INFO @ Mon, 03 Jun 2019 05:25:43: start X-correlation... INFO @ Mon, 03 Jun 2019 05:25:43: end of X-cor INFO @ Mon, 03 Jun 2019 05:25:43: #2 finished! INFO @ Mon, 03 Jun 2019 05:25:43: #2 predicted fragment length is 95 bps INFO @ Mon, 03 Jun 2019 05:25:43: #2 alternative fragment length(s) may be 95 bps INFO @ Mon, 03 Jun 2019 05:25:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX186112/SRX186112.05_model.r WARNING @ Mon, 03 Jun 2019 05:25:43: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:25:43: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Mon, 03 Jun 2019 05:25:43: #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 05:25:43: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:25:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:25:44: #2 number of paired peaks: 756 WARNING @ Mon, 03 Jun 2019 05:25:44: Fewer paired peaks (756) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 756 pairs to build model! INFO @ Mon, 03 Jun 2019 05:25:44: start model_add_line... INFO @ Mon, 03 Jun 2019 05:25:44: start X-correlation... INFO @ Mon, 03 Jun 2019 05:25:44: end of X-cor INFO @ Mon, 03 Jun 2019 05:25:44: #2 finished! INFO @ Mon, 03 Jun 2019 05:25:44: #2 predicted fragment length is 95 bps INFO @ Mon, 03 Jun 2019 05:25:44: #2 alternative fragment length(s) may be 95 bps INFO @ Mon, 03 Jun 2019 05:25:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX186112/SRX186112.20_model.r WARNING @ Mon, 03 Jun 2019 05:25:44: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:25:44: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Mon, 03 Jun 2019 05:25:44: #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 05:25:44: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:25:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:25:49: 9000000 INFO @ Mon, 03 Jun 2019 05:25:52: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 05:25:52: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 05:25:52: #1 total tags in treatment: 9287834 INFO @ Mon, 03 Jun 2019 05:25:52: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:25:52: #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 05:25:52: #1 tags after filtering in treatment: 9287834 INFO @ Mon, 03 Jun 2019 05:25:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:25:52: #1 finished! INFO @ Mon, 03 Jun 2019 05:25:52: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:25:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:25:53: #2 number of paired peaks: 756 WARNING @ Mon, 03 Jun 2019 05:25:53: Fewer paired peaks (756) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 756 pairs to build model! INFO @ Mon, 03 Jun 2019 05:25:53: start model_add_line... INFO @ Mon, 03 Jun 2019 05:25:53: start X-correlation... INFO @ Mon, 03 Jun 2019 05:25:53: end of X-cor INFO @ Mon, 03 Jun 2019 05:25:53: #2 finished! INFO @ Mon, 03 Jun 2019 05:25:53: #2 predicted fragment length is 95 bps INFO @ Mon, 03 Jun 2019 05:25:53: #2 alternative fragment length(s) may be 95 bps INFO @ Mon, 03 Jun 2019 05:25:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX186112/SRX186112.10_model.r WARNING @ Mon, 03 Jun 2019 05:25:53: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:25:53: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Mon, 03 Jun 2019 05:25:53: #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 05:25:53: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:25:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:26:11: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:26:11: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:26:20: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:26:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX186112/SRX186112.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:26:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX186112/SRX186112.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:26:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX186112/SRX186112.05_summits.bed INFO @ Mon, 03 Jun 2019 05:26:24: Done! pass1 - making usageList (15 chroms): 2 millis INFO @ Mon, 03 Jun 2019 05:26:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX186112/SRX186112.20_peaks.xls pass2 - checking and writing primary data (6569 records, 4 fields): 9 millis INFO @ Mon, 03 Jun 2019 05:26:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX186112/SRX186112.20_peaks.narrowPeak CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:26:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX186112/SRX186112.20_summits.bed INFO @ Mon, 03 Jun 2019 05:26:24: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1708 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:26:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX186112/SRX186112.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:26:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX186112/SRX186112.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:26:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX186112/SRX186112.10_summits.bed INFO @ Mon, 03 Jun 2019 05:26:34: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3189 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。