Job ID = 1295491 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 47,987,333 reads read : 47,987,333 reads written : 47,987,333 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: 00:20:50 47987333 reads; of these: 47987333 (100.00%) were unpaired; of these: 37337761 (77.81%) aligned 0 times 7347676 (15.31%) aligned exactly 1 time 3301896 (6.88%) aligned >1 times 22.19% overall alignment rate Time searching: 00:20:50 Overall time: 00:20:50 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] 2036850 / 10649572 = 0.1913 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 14:29:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX348460/SRX348460.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX348460/SRX348460.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX348460/SRX348460.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX348460/SRX348460.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 14:29:54: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:29:54: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:29:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX348460/SRX348460.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX348460/SRX348460.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX348460/SRX348460.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX348460/SRX348460.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 14:29:55: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:29:55: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:29:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX348460/SRX348460.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX348460/SRX348460.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX348460/SRX348460.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX348460/SRX348460.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 14:29:55: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:29:55: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:30:05: 1000000 INFO @ Mon, 03 Jun 2019 14:30:06: 1000000 INFO @ Mon, 03 Jun 2019 14:30:08: 1000000 INFO @ Mon, 03 Jun 2019 14:30:14: 2000000 INFO @ Mon, 03 Jun 2019 14:30:18: 2000000 INFO @ Mon, 03 Jun 2019 14:30:20: 2000000 INFO @ Mon, 03 Jun 2019 14:30:24: 3000000 INFO @ Mon, 03 Jun 2019 14:30:29: 3000000 INFO @ Mon, 03 Jun 2019 14:30:32: 3000000 INFO @ Mon, 03 Jun 2019 14:30:33: 4000000 INFO @ Mon, 03 Jun 2019 14:30:40: 4000000 INFO @ Mon, 03 Jun 2019 14:30:43: 5000000 INFO @ Mon, 03 Jun 2019 14:30:45: 4000000 INFO @ Mon, 03 Jun 2019 14:30:52: 5000000 INFO @ Mon, 03 Jun 2019 14:30:52: 6000000 INFO @ Mon, 03 Jun 2019 14:30:58: 5000000 INFO @ Mon, 03 Jun 2019 14:31:03: 7000000 INFO @ Mon, 03 Jun 2019 14:31:03: 6000000 INFO @ Mon, 03 Jun 2019 14:31:10: 6000000 INFO @ Mon, 03 Jun 2019 14:31:12: 8000000 INFO @ Mon, 03 Jun 2019 14:31:14: 7000000 INFO @ Mon, 03 Jun 2019 14:31:18: #1 tag size is determined as 100 bps INFO @ Mon, 03 Jun 2019 14:31:18: #1 tag size = 100 INFO @ Mon, 03 Jun 2019 14:31:18: #1 total tags in treatment: 8612722 INFO @ Mon, 03 Jun 2019 14:31:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:31:18: #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 14:31:19: #1 tags after filtering in treatment: 8612722 INFO @ Mon, 03 Jun 2019 14:31:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:31:19: #1 finished! INFO @ Mon, 03 Jun 2019 14:31:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:31:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:31:19: #2 number of paired peaks: 285 WARNING @ Mon, 03 Jun 2019 14:31:19: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Mon, 03 Jun 2019 14:31:19: start model_add_line... INFO @ Mon, 03 Jun 2019 14:31:19: start X-correlation... INFO @ Mon, 03 Jun 2019 14:31:19: end of X-cor INFO @ Mon, 03 Jun 2019 14:31:19: #2 finished! INFO @ Mon, 03 Jun 2019 14:31:19: #2 predicted fragment length is 84 bps INFO @ Mon, 03 Jun 2019 14:31:19: #2 alternative fragment length(s) may be 84 bps INFO @ Mon, 03 Jun 2019 14:31:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX348460/SRX348460.10_model.r WARNING @ Mon, 03 Jun 2019 14:31:19: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 14:31:19: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Mon, 03 Jun 2019 14:31:19: #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 14:31:19: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:31:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:31:23: 7000000 INFO @ Mon, 03 Jun 2019 14:31:26: 8000000 INFO @ Mon, 03 Jun 2019 14:31:32: #1 tag size is determined as 100 bps INFO @ Mon, 03 Jun 2019 14:31:32: #1 tag size = 100 INFO @ Mon, 03 Jun 2019 14:31:32: #1 total tags in treatment: 8612722 INFO @ Mon, 03 Jun 2019 14:31:32: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:31:32: #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 14:31:33: #1 tags after filtering in treatment: 8612722 INFO @ Mon, 03 Jun 2019 14:31:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:31:33: #1 finished! INFO @ Mon, 03 Jun 2019 14:31:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:31:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:31:33: #2 number of paired peaks: 285 WARNING @ Mon, 03 Jun 2019 14:31:33: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Mon, 03 Jun 2019 14:31:33: start model_add_line... INFO @ Mon, 03 Jun 2019 14:31:33: start X-correlation... INFO @ Mon, 03 Jun 2019 14:31:33: end of X-cor INFO @ Mon, 03 Jun 2019 14:31:33: #2 finished! INFO @ Mon, 03 Jun 2019 14:31:33: #2 predicted fragment length is 84 bps INFO @ Mon, 03 Jun 2019 14:31:33: #2 alternative fragment length(s) may be 84 bps INFO @ Mon, 03 Jun 2019 14:31:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX348460/SRX348460.20_model.r WARNING @ Mon, 03 Jun 2019 14:31:33: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 14:31:33: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Mon, 03 Jun 2019 14:31:33: #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 14:31:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:31:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:31:35: 8000000 INFO @ Mon, 03 Jun 2019 14:31:42: #1 tag size is determined as 100 bps INFO @ Mon, 03 Jun 2019 14:31:42: #1 tag size = 100 INFO @ Mon, 03 Jun 2019 14:31:42: #1 total tags in treatment: 8612722 INFO @ Mon, 03 Jun 2019 14:31:42: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:31:42: #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 14:31:42: #1 tags after filtering in treatment: 8612722 INFO @ Mon, 03 Jun 2019 14:31:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:31:42: #1 finished! INFO @ Mon, 03 Jun 2019 14:31:42: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:31:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:31:43: #2 number of paired peaks: 285 WARNING @ Mon, 03 Jun 2019 14:31:43: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Mon, 03 Jun 2019 14:31:43: start model_add_line... INFO @ Mon, 03 Jun 2019 14:31:43: start X-correlation... INFO @ Mon, 03 Jun 2019 14:31:43: end of X-cor INFO @ Mon, 03 Jun 2019 14:31:43: #2 finished! INFO @ Mon, 03 Jun 2019 14:31:43: #2 predicted fragment length is 84 bps INFO @ Mon, 03 Jun 2019 14:31:43: #2 alternative fragment length(s) may be 84 bps INFO @ Mon, 03 Jun 2019 14:31:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX348460/SRX348460.05_model.r WARNING @ Mon, 03 Jun 2019 14:31:43: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 14:31:43: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Mon, 03 Jun 2019 14:31:43: #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 14:31:43: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:31:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:31:44: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:31:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX348460/SRX348460.10_peaks.xls INFO @ Mon, 03 Jun 2019 14:31:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX348460/SRX348460.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:31:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX348460/SRX348460.10_summits.bed INFO @ Mon, 03 Jun 2019 14:31:56: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2717 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:31:58: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:32:08: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:32:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX348460/SRX348460.20_peaks.xls INFO @ Mon, 03 Jun 2019 14:32:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX348460/SRX348460.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:32:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX348460/SRX348460.20_summits.bed INFO @ Mon, 03 Jun 2019 14:32:10: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (926 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:32:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX348460/SRX348460.05_peaks.xls INFO @ Mon, 03 Jun 2019 14:32:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX348460/SRX348460.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:32:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX348460/SRX348460.05_summits.bed INFO @ Mon, 03 Jun 2019 14:32:20: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (3908 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。