Job ID = 1294285 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,313,650 reads read : 3,313,650 reads written : 3,313,650 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:35 3313650 reads; of these: 3313650 (100.00%) were unpaired; of these: 1151648 (34.75%) aligned 0 times 2007356 (60.58%) aligned exactly 1 time 154646 (4.67%) aligned >1 times 65.25% overall alignment rate Time searching: 00:00:36 Overall time: 00:00:36 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] 178252 / 2162002 = 0.0824 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 06:04:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX231857/SRX231857.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX231857/SRX231857.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX231857/SRX231857.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX231857/SRX231857.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 06:04:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:04:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:04:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX231857/SRX231857.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX231857/SRX231857.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX231857/SRX231857.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX231857/SRX231857.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 06:04:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:04:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:04:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX231857/SRX231857.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX231857/SRX231857.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX231857/SRX231857.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX231857/SRX231857.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 06:04:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:04:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:05:05: 1000000 INFO @ Mon, 03 Jun 2019 06:05:05: 1000000 INFO @ Mon, 03 Jun 2019 06:05:06: 1000000 INFO @ Mon, 03 Jun 2019 06:05:12: #1 tag size is determined as 33 bps INFO @ Mon, 03 Jun 2019 06:05:12: #1 tag size = 33 INFO @ Mon, 03 Jun 2019 06:05:12: #1 total tags in treatment: 1983750 INFO @ Mon, 03 Jun 2019 06:05:12: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:05:12: #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 06:05:12: #1 tags after filtering in treatment: 1983750 INFO @ Mon, 03 Jun 2019 06:05:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:05:12: #1 finished! INFO @ Mon, 03 Jun 2019 06:05:12: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:05:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:05:13: #2 number of paired peaks: 463 WARNING @ Mon, 03 Jun 2019 06:05:13: Fewer paired peaks (463) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 463 pairs to build model! INFO @ Mon, 03 Jun 2019 06:05:13: start model_add_line... INFO @ Mon, 03 Jun 2019 06:05:13: start X-correlation... INFO @ Mon, 03 Jun 2019 06:05:13: end of X-cor INFO @ Mon, 03 Jun 2019 06:05:13: #2 finished! INFO @ Mon, 03 Jun 2019 06:05:13: #2 predicted fragment length is 156 bps INFO @ Mon, 03 Jun 2019 06:05:13: #2 alternative fragment length(s) may be 156,324 bps INFO @ Mon, 03 Jun 2019 06:05:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX231857/SRX231857.20_model.r INFO @ Mon, 03 Jun 2019 06:05:13: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:05:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:05:13: #1 tag size is determined as 33 bps INFO @ Mon, 03 Jun 2019 06:05:13: #1 tag size = 33 INFO @ Mon, 03 Jun 2019 06:05:13: #1 total tags in treatment: 1983750 INFO @ Mon, 03 Jun 2019 06:05:13: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:05:13: #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 06:05:13: #1 tags after filtering in treatment: 1983750 INFO @ Mon, 03 Jun 2019 06:05:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:05:13: #1 finished! INFO @ Mon, 03 Jun 2019 06:05:13: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:05:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:05:13: #2 number of paired peaks: 463 WARNING @ Mon, 03 Jun 2019 06:05:13: Fewer paired peaks (463) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 463 pairs to build model! INFO @ Mon, 03 Jun 2019 06:05:13: start model_add_line... INFO @ Mon, 03 Jun 2019 06:05:13: start X-correlation... INFO @ Mon, 03 Jun 2019 06:05:13: end of X-cor INFO @ Mon, 03 Jun 2019 06:05:13: #2 finished! INFO @ Mon, 03 Jun 2019 06:05:13: #2 predicted fragment length is 156 bps INFO @ Mon, 03 Jun 2019 06:05:13: #2 alternative fragment length(s) may be 156,324 bps INFO @ Mon, 03 Jun 2019 06:05:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX231857/SRX231857.10_model.r INFO @ Mon, 03 Jun 2019 06:05:13: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:05:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:05:14: #1 tag size is determined as 33 bps INFO @ Mon, 03 Jun 2019 06:05:14: #1 tag size = 33 INFO @ Mon, 03 Jun 2019 06:05:14: #1 total tags in treatment: 1983750 INFO @ Mon, 03 Jun 2019 06:05:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:05:14: #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 06:05:14: #1 tags after filtering in treatment: 1983750 INFO @ Mon, 03 Jun 2019 06:05:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:05:14: #1 finished! INFO @ Mon, 03 Jun 2019 06:05:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:05:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:05:15: #2 number of paired peaks: 463 WARNING @ Mon, 03 Jun 2019 06:05:15: Fewer paired peaks (463) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 463 pairs to build model! INFO @ Mon, 03 Jun 2019 06:05:15: start model_add_line... INFO @ Mon, 03 Jun 2019 06:05:15: start X-correlation... INFO @ Mon, 03 Jun 2019 06:05:15: end of X-cor INFO @ Mon, 03 Jun 2019 06:05:15: #2 finished! INFO @ Mon, 03 Jun 2019 06:05:15: #2 predicted fragment length is 156 bps INFO @ Mon, 03 Jun 2019 06:05:15: #2 alternative fragment length(s) may be 156,324 bps INFO @ Mon, 03 Jun 2019 06:05:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX231857/SRX231857.05_model.r INFO @ Mon, 03 Jun 2019 06:05:15: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:05:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:05:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:05:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:05:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:05:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX231857/SRX231857.20_peaks.xls INFO @ Mon, 03 Jun 2019 06:05:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX231857/SRX231857.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:05:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX231857/SRX231857.20_summits.bed INFO @ Mon, 03 Jun 2019 06:05:22: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (12 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:05:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX231857/SRX231857.10_peaks.xls INFO @ Mon, 03 Jun 2019 06:05:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX231857/SRX231857.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:05:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX231857/SRX231857.10_summits.bed INFO @ Mon, 03 Jun 2019 06:05:22: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (115 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:05:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX231857/SRX231857.05_peaks.xls INFO @ Mon, 03 Jun 2019 06:05:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX231857/SRX231857.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:05:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX231857/SRX231857.05_summits.bed INFO @ Mon, 03 Jun 2019 06:05:24: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (737 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。