Job ID = 2590898 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,221,792 reads read : 12,221,792 reads written : 12,221,792 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: 00:02:25 12221792 reads; of these: 12221792 (100.00%) were unpaired; of these: 2745777 (22.47%) aligned 0 times 9072035 (74.23%) aligned exactly 1 time 403980 (3.31%) aligned >1 times 77.53% overall alignment rate Time searching: 00:02:25 Overall time: 00:02:25 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] 9148709 / 9476015 = 0.9655 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 @ Tue, 13 Aug 2019 00:00:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5360580/SRX5360580.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5360580/SRX5360580.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5360580/SRX5360580.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5360580/SRX5360580.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 @ Tue, 13 Aug 2019 00:00:16: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:00:16: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:00:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5360580/SRX5360580.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5360580/SRX5360580.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5360580/SRX5360580.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5360580/SRX5360580.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 @ Tue, 13 Aug 2019 00:00:17: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:00:17: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:00:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5360580/SRX5360580.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5360580/SRX5360580.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5360580/SRX5360580.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5360580/SRX5360580.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 @ Tue, 13 Aug 2019 00:00:18: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:00:18: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:00:19: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:00:19: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:00:19: #1 total tags in treatment: 327306 INFO @ Tue, 13 Aug 2019 00:00:19: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:00:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:00:19: #1 tags after filtering in treatment: 327306 INFO @ Tue, 13 Aug 2019 00:00:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:00:19: #1 finished! INFO @ Tue, 13 Aug 2019 00:00:19: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:00:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:00:19: #2 number of paired peaks: 807 WARNING @ Tue, 13 Aug 2019 00:00:19: Fewer paired peaks (807) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 807 pairs to build model! INFO @ Tue, 13 Aug 2019 00:00:19: start model_add_line... INFO @ Tue, 13 Aug 2019 00:00:19: start X-correlation... INFO @ Tue, 13 Aug 2019 00:00:19: end of X-cor INFO @ Tue, 13 Aug 2019 00:00:19: #2 finished! INFO @ Tue, 13 Aug 2019 00:00:19: #2 predicted fragment length is 49 bps INFO @ Tue, 13 Aug 2019 00:00:19: #2 alternative fragment length(s) may be 49,474 bps INFO @ Tue, 13 Aug 2019 00:00:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5360580/SRX5360580.05_model.r WARNING @ Tue, 13 Aug 2019 00:00:19: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:00:19: #2 You may need to consider one of the other alternative d(s): 49,474 WARNING @ Tue, 13 Aug 2019 00:00:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 00:00:19: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:00:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:00:20: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:00:20: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:00:20: #1 total tags in treatment: 327306 INFO @ Tue, 13 Aug 2019 00:00:20: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:00:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:00:20: #1 tags after filtering in treatment: 327306 INFO @ Tue, 13 Aug 2019 00:00:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:00:20: #1 finished! INFO @ Tue, 13 Aug 2019 00:00:20: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:00:20: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 13 Aug 2019 00:00:20: #2 number of paired peaks: 807 WARNING @ Tue, 13 Aug 2019 00:00:20: Fewer paired peaks (807) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 807 pairs to build model! INFO @ Tue, 13 Aug 2019 00:00:20: start model_add_line... INFO @ Tue, 13 Aug 2019 00:00:20: start X-correlation... INFO @ Tue, 13 Aug 2019 00:00:20: end of X-cor INFO @ Tue, 13 Aug 2019 00:00:20: #2 finished! INFO @ Tue, 13 Aug 2019 00:00:20: #2 predicted fragment length is 49 bps INFO @ Tue, 13 Aug 2019 00:00:20: #2 alternative fragment length(s) may be 49,474 bps INFO @ Tue, 13 Aug 2019 00:00:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5360580/SRX5360580.10_model.r WARNING @ Tue, 13 Aug 2019 00:00:20: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:00:20: #2 You may need to consider one of the other alternative d(s): 49,474 WARNING @ Tue, 13 Aug 2019 00:00:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 00:00:20: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:00:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:00:20: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 13 Aug 2019 00:00:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5360580/SRX5360580.05_peaks.xls INFO @ Tue, 13 Aug 2019 00:00:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5360580/SRX5360580.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:00:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5360580/SRX5360580.05_summits.bed INFO @ Tue, 13 Aug 2019 00:00:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (456 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:00:21: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:00:21: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:00:21: #1 total tags in treatment: 327306 INFO @ Tue, 13 Aug 2019 00:00:21: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:00:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:00:21: #1 tags after filtering in treatment: 327306 INFO @ Tue, 13 Aug 2019 00:00:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:00:21: #1 finished! INFO @ Tue, 13 Aug 2019 00:00:21: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:00:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:00:21: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:00:21: #2 number of paired peaks: 807 WARNING @ Tue, 13 Aug 2019 00:00:21: Fewer paired peaks (807) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 807 pairs to build model! INFO @ Tue, 13 Aug 2019 00:00:21: start model_add_line... INFO @ Tue, 13 Aug 2019 00:00:21: start X-correlation... INFO @ Tue, 13 Aug 2019 00:00:21: end of X-cor INFO @ Tue, 13 Aug 2019 00:00:21: #2 finished! INFO @ Tue, 13 Aug 2019 00:00:21: #2 predicted fragment length is 49 bps INFO @ Tue, 13 Aug 2019 00:00:21: #2 alternative fragment length(s) may be 49,474 bps INFO @ Tue, 13 Aug 2019 00:00:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5360580/SRX5360580.20_model.r WARNING @ Tue, 13 Aug 2019 00:00:21: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:00:21: #2 You may need to consider one of the other alternative d(s): 49,474 WARNING @ Tue, 13 Aug 2019 00:00:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 00:00:21: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:00:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:00:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5360580/SRX5360580.10_peaks.xls INFO @ Tue, 13 Aug 2019 00:00:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5360580/SRX5360580.10_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:00:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5360580/SRX5360580.10_summits.bed INFO @ Tue, 13 Aug 2019 00:00:21: Done! pass1 - making usageList (5 chroms): 2 millis pass2 - checking and writing primary data (333 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:00:22: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:00:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5360580/SRX5360580.20_peaks.xls INFO @ Tue, 13 Aug 2019 00:00:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5360580/SRX5360580.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:00:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5360580/SRX5360580.20_summits.bed INFO @ Tue, 13 Aug 2019 00:00:22: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (232 records, 4 fields): 2 millis CompletedMACS2peakCalling