Job ID = 2590905 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,550,088 reads read : 5,550,088 reads written : 5,550,088 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: 00:01:04 5550088 reads; of these: 5550088 (100.00%) were unpaired; of these: 1815076 (32.70%) aligned 0 times 3484094 (62.78%) aligned exactly 1 time 250918 (4.52%) aligned >1 times 67.30% overall alignment rate Time searching: 00:01:04 Overall time: 00:01:04 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] 3271724 / 3735012 = 0.8760 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 23:56:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5360586/SRX5360586.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5360586/SRX5360586.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5360586/SRX5360586.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5360586/SRX5360586.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 23:56:11: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:56:11: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:56:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5360586/SRX5360586.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5360586/SRX5360586.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5360586/SRX5360586.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5360586/SRX5360586.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 23:56:12: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:56:12: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:56:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5360586/SRX5360586.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5360586/SRX5360586.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5360586/SRX5360586.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5360586/SRX5360586.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 23:56:13: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:56:13: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:56:14: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:56:14: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:56:14: #1 total tags in treatment: 463288 INFO @ Mon, 12 Aug 2019 23:56:14: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:56:14: #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 23:56:14: #1 tags after filtering in treatment: 463288 INFO @ Mon, 12 Aug 2019 23:56:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:56:14: #1 finished! INFO @ Mon, 12 Aug 2019 23:56:14: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:56:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:56:14: #2 number of paired peaks: 1341 INFO @ Mon, 12 Aug 2019 23:56:14: start model_add_line... INFO @ Mon, 12 Aug 2019 23:56:15: start X-correlation... INFO @ Mon, 12 Aug 2019 23:56:15: end of X-cor INFO @ Mon, 12 Aug 2019 23:56:15: #2 finished! INFO @ Mon, 12 Aug 2019 23:56:15: #2 predicted fragment length is 52 bps INFO @ Mon, 12 Aug 2019 23:56:15: #2 alternative fragment length(s) may be 52 bps INFO @ Mon, 12 Aug 2019 23:56:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5360586/SRX5360586.05_model.r WARNING @ Mon, 12 Aug 2019 23:56:15: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:56:15: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Mon, 12 Aug 2019 23:56:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:56:15: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:56:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:56:16: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:56:16: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:56:16: #1 total tags in treatment: 463288 INFO @ Mon, 12 Aug 2019 23:56:16: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:56:16: #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 23:56:16: #1 tags after filtering in treatment: 463288 INFO @ Mon, 12 Aug 2019 23:56:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:56:16: #1 finished! INFO @ Mon, 12 Aug 2019 23:56:16: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:56:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:56:16: #2 number of paired peaks: 1341 INFO @ Mon, 12 Aug 2019 23:56:16: start model_add_line... INFO @ Mon, 12 Aug 2019 23:56:16: start X-correlation... INFO @ Mon, 12 Aug 2019 23:56:16: end of X-cor INFO @ Mon, 12 Aug 2019 23:56:16: #2 finished! INFO @ Mon, 12 Aug 2019 23:56:16: #2 predicted fragment length is 52 bps INFO @ Mon, 12 Aug 2019 23:56:16: #2 alternative fragment length(s) may be 52 bps INFO @ Mon, 12 Aug 2019 23:56:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5360586/SRX5360586.10_model.r WARNING @ Mon, 12 Aug 2019 23:56:16: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:56:16: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Mon, 12 Aug 2019 23:56:16: #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 23:56:16: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:56:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:56:16: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:56:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5360586/SRX5360586.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:56:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5360586/SRX5360586.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:56:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5360586/SRX5360586.05_summits.bed INFO @ Mon, 12 Aug 2019 23:56:17: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (429 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:56:17: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:56:17: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:56:17: #1 total tags in treatment: 463288 INFO @ Mon, 12 Aug 2019 23:56:17: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:56:17: #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 23:56:17: #1 tags after filtering in treatment: 463288 INFO @ Mon, 12 Aug 2019 23:56:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:56:17: #1 finished! INFO @ Mon, 12 Aug 2019 23:56:17: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:56:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:56:17: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:56:17: #2 number of paired peaks: 1341 INFO @ Mon, 12 Aug 2019 23:56:17: start model_add_line... INFO @ Mon, 12 Aug 2019 23:56:18: start X-correlation... INFO @ Mon, 12 Aug 2019 23:56:18: end of X-cor INFO @ Mon, 12 Aug 2019 23:56:18: #2 finished! INFO @ Mon, 12 Aug 2019 23:56:18: #2 predicted fragment length is 52 bps INFO @ Mon, 12 Aug 2019 23:56:18: #2 alternative fragment length(s) may be 52 bps INFO @ Mon, 12 Aug 2019 23:56:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5360586/SRX5360586.20_model.r WARNING @ Mon, 12 Aug 2019 23:56:18: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:56:18: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Mon, 12 Aug 2019 23:56:18: #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 23:56:18: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:56:18: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 12 Aug 2019 23:56:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5360586/SRX5360586.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:56:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5360586/SRX5360586.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:56:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5360586/SRX5360586.10_summits.bed INFO @ Mon, 12 Aug 2019 23:56:18: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (270 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Mon, 12 Aug 2019 23:56:19: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:56:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5360586/SRX5360586.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:56:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5360586/SRX5360586.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:56:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5360586/SRX5360586.20_summits.bed INFO @ Mon, 12 Aug 2019 23:56:20: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (149 records, 4 fields): 1 millis CompletedMACS2peakCalling