Job ID = 1308866 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 34,877,874 reads read : 69,755,748 reads written : 34,877,874 reads 0-length : 34,877,874 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: 00:14:49 34877874 reads; of these: 34877874 (100.00%) were unpaired; of these: 6603590 (18.93%) aligned 0 times 20103245 (57.64%) aligned exactly 1 time 8171039 (23.43%) aligned >1 times 81.07% overall alignment rate Time searching: 00:14:49 Overall time: 00:14:49 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] 18833211 / 28274284 = 0.6661 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 23:29:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5661477/SRX5661477.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5661477/SRX5661477.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5661477/SRX5661477.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5661477/SRX5661477.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 23:29:49: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:29:49: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:29:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5661477/SRX5661477.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5661477/SRX5661477.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5661477/SRX5661477.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5661477/SRX5661477.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 23:29:49: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:29:49: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:29:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5661477/SRX5661477.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5661477/SRX5661477.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5661477/SRX5661477.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5661477/SRX5661477.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 23:29:49: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:29:49: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:29:58: 1000000 INFO @ Mon, 03 Jun 2019 23:29:58: 1000000 INFO @ Mon, 03 Jun 2019 23:29:58: 1000000 INFO @ Mon, 03 Jun 2019 23:30:07: 2000000 INFO @ Mon, 03 Jun 2019 23:30:07: 2000000 INFO @ Mon, 03 Jun 2019 23:30:08: 2000000 INFO @ Mon, 03 Jun 2019 23:30:16: 3000000 INFO @ Mon, 03 Jun 2019 23:30:17: 3000000 INFO @ Mon, 03 Jun 2019 23:30:18: 3000000 INFO @ Mon, 03 Jun 2019 23:30:25: 4000000 INFO @ Mon, 03 Jun 2019 23:30:26: 4000000 INFO @ Mon, 03 Jun 2019 23:30:27: 4000000 INFO @ Mon, 03 Jun 2019 23:30:34: 5000000 INFO @ Mon, 03 Jun 2019 23:30:35: 5000000 INFO @ Mon, 03 Jun 2019 23:30:35: 5000000 INFO @ Mon, 03 Jun 2019 23:30:43: 6000000 INFO @ Mon, 03 Jun 2019 23:30:44: 6000000 INFO @ Mon, 03 Jun 2019 23:30:44: 6000000 INFO @ Mon, 03 Jun 2019 23:30:52: 7000000 INFO @ Mon, 03 Jun 2019 23:30:52: 7000000 INFO @ Mon, 03 Jun 2019 23:30:53: 7000000 INFO @ Mon, 03 Jun 2019 23:31:00: 8000000 INFO @ Mon, 03 Jun 2019 23:31:01: 8000000 INFO @ Mon, 03 Jun 2019 23:31:01: 8000000 INFO @ Mon, 03 Jun 2019 23:31:08: 9000000 INFO @ Mon, 03 Jun 2019 23:31:10: 9000000 INFO @ Mon, 03 Jun 2019 23:31:10: 9000000 INFO @ Mon, 03 Jun 2019 23:31:12: #1 tag size is determined as 62 bps INFO @ Mon, 03 Jun 2019 23:31:12: #1 tag size = 62 INFO @ Mon, 03 Jun 2019 23:31:12: #1 total tags in treatment: 9441073 INFO @ Mon, 03 Jun 2019 23:31:12: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:31:12: #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 23:31:12: #1 tags after filtering in treatment: 9441073 INFO @ Mon, 03 Jun 2019 23:31:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:31:12: #1 finished! INFO @ Mon, 03 Jun 2019 23:31:12: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:31:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:31:13: #2 number of paired peaks: 609 WARNING @ Mon, 03 Jun 2019 23:31:13: Fewer paired peaks (609) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 609 pairs to build model! INFO @ Mon, 03 Jun 2019 23:31:13: start model_add_line... INFO @ Mon, 03 Jun 2019 23:31:13: start X-correlation... INFO @ Mon, 03 Jun 2019 23:31:13: end of X-cor INFO @ Mon, 03 Jun 2019 23:31:13: #2 finished! INFO @ Mon, 03 Jun 2019 23:31:13: #2 predicted fragment length is 57 bps INFO @ Mon, 03 Jun 2019 23:31:13: #2 alternative fragment length(s) may be 57 bps INFO @ Mon, 03 Jun 2019 23:31:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5661477/SRX5661477.05_model.r WARNING @ Mon, 03 Jun 2019 23:31:13: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:31:13: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Mon, 03 Jun 2019 23:31:13: #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 23:31:13: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:31:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:31:13: #1 tag size is determined as 62 bps INFO @ Mon, 03 Jun 2019 23:31:13: #1 tag size = 62 INFO @ Mon, 03 Jun 2019 23:31:13: #1 total tags in treatment: 9441073 INFO @ Mon, 03 Jun 2019 23:31:13: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:31:13: #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 23:31:14: #1 tags after filtering in treatment: 9441073 INFO @ Mon, 03 Jun 2019 23:31:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:31:14: #1 finished! INFO @ Mon, 03 Jun 2019 23:31:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:31:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:31:14: #1 tag size is determined as 62 bps INFO @ Mon, 03 Jun 2019 23:31:14: #1 tag size = 62 INFO @ Mon, 03 Jun 2019 23:31:14: #1 total tags in treatment: 9441073 INFO @ Mon, 03 Jun 2019 23:31:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:31:14: #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 23:31:14: #1 tags after filtering in treatment: 9441073 INFO @ Mon, 03 Jun 2019 23:31:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:31:14: #1 finished! INFO @ Mon, 03 Jun 2019 23:31:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:31:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:31:15: #2 number of paired peaks: 609 WARNING @ Mon, 03 Jun 2019 23:31:15: Fewer paired peaks (609) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 609 pairs to build model! INFO @ Mon, 03 Jun 2019 23:31:15: start model_add_line... INFO @ Mon, 03 Jun 2019 23:31:15: start X-correlation... INFO @ Mon, 03 Jun 2019 23:31:15: end of X-cor INFO @ Mon, 03 Jun 2019 23:31:15: #2 finished! INFO @ Mon, 03 Jun 2019 23:31:15: #2 predicted fragment length is 57 bps INFO @ Mon, 03 Jun 2019 23:31:15: #2 alternative fragment length(s) may be 57 bps INFO @ Mon, 03 Jun 2019 23:31:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5661477/SRX5661477.20_model.r WARNING @ Mon, 03 Jun 2019 23:31:15: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:31:15: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Mon, 03 Jun 2019 23:31:15: #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 23:31:15: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:31:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:31:15: #2 number of paired peaks: 609 WARNING @ Mon, 03 Jun 2019 23:31:15: Fewer paired peaks (609) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 609 pairs to build model! INFO @ Mon, 03 Jun 2019 23:31:15: start model_add_line... INFO @ Mon, 03 Jun 2019 23:31:15: start X-correlation... INFO @ Mon, 03 Jun 2019 23:31:15: end of X-cor INFO @ Mon, 03 Jun 2019 23:31:15: #2 finished! INFO @ Mon, 03 Jun 2019 23:31:15: #2 predicted fragment length is 57 bps INFO @ Mon, 03 Jun 2019 23:31:15: #2 alternative fragment length(s) may be 57 bps INFO @ Mon, 03 Jun 2019 23:31:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5661477/SRX5661477.10_model.r WARNING @ Mon, 03 Jun 2019 23:31:15: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:31:15: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Mon, 03 Jun 2019 23:31:15: #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 23:31:15: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:31:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:31:40: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:31:42: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:31:42: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:31:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5661477/SRX5661477.05_peaks.xls INFO @ Mon, 03 Jun 2019 23:31:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5661477/SRX5661477.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:31:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5661477/SRX5661477.05_summits.bed INFO @ Mon, 03 Jun 2019 23:31:54: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3184 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:31:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5661477/SRX5661477.20_peaks.xls INFO @ Mon, 03 Jun 2019 23:31:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5661477/SRX5661477.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:31:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5661477/SRX5661477.20_summits.bed INFO @ Mon, 03 Jun 2019 23:31:56: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1073 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:31:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5661477/SRX5661477.10_peaks.xls INFO @ Mon, 03 Jun 2019 23:31:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5661477/SRX5661477.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:31:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5661477/SRX5661477.10_summits.bed INFO @ Mon, 03 Jun 2019 23:31:56: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1638 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。