Job ID = 1292034 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,374,012 reads read : 13,374,012 reads written : 13,374,012 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: 00:01:32 13374012 reads; of these: 13374012 (100.00%) were unpaired; of these: 7111854 (53.18%) aligned 0 times 5025438 (37.58%) aligned exactly 1 time 1236720 (9.25%) aligned >1 times 46.82% overall alignment rate Time searching: 00:01:32 Overall time: 00:01:32 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 1499411 / 6262158 = 0.2394 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 @ Sun, 02 Jun 2019 17:18:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX323680/SRX323680.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX323680/SRX323680.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX323680/SRX323680.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX323680/SRX323680.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 02 Jun 2019 17:18:32: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:18:32: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:18:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX323680/SRX323680.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX323680/SRX323680.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX323680/SRX323680.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX323680/SRX323680.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 02 Jun 2019 17:18:32: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:18:32: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:18:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX323680/SRX323680.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX323680/SRX323680.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX323680/SRX323680.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX323680/SRX323680.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 02 Jun 2019 17:18:32: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:18:32: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:18:41: 1000000 INFO @ Sun, 02 Jun 2019 17:18:42: 1000000 INFO @ Sun, 02 Jun 2019 17:18:44: 1000000 INFO @ Sun, 02 Jun 2019 17:18:49: 2000000 INFO @ Sun, 02 Jun 2019 17:18:52: 2000000 INFO @ Sun, 02 Jun 2019 17:18:55: 2000000 INFO @ Sun, 02 Jun 2019 17:18:58: 3000000 INFO @ Sun, 02 Jun 2019 17:19:02: 3000000 INFO @ Sun, 02 Jun 2019 17:19:06: 4000000 INFO @ Sun, 02 Jun 2019 17:19:06: 3000000 INFO @ Sun, 02 Jun 2019 17:19:12: 4000000 INFO @ Sun, 02 Jun 2019 17:19:12: #1 tag size is determined as 35 bps INFO @ Sun, 02 Jun 2019 17:19:12: #1 tag size = 35 INFO @ Sun, 02 Jun 2019 17:19:12: #1 total tags in treatment: 4762747 INFO @ Sun, 02 Jun 2019 17:19:12: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:19:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 17:19:12: #1 tags after filtering in treatment: 4762747 INFO @ Sun, 02 Jun 2019 17:19:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:19:12: #1 finished! INFO @ Sun, 02 Jun 2019 17:19:12: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:19:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:19:13: #2 number of paired peaks: 339 WARNING @ Sun, 02 Jun 2019 17:19:13: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Sun, 02 Jun 2019 17:19:13: start model_add_line... INFO @ Sun, 02 Jun 2019 17:19:13: start X-correlation... INFO @ Sun, 02 Jun 2019 17:19:13: end of X-cor INFO @ Sun, 02 Jun 2019 17:19:13: #2 finished! INFO @ Sun, 02 Jun 2019 17:19:13: #2 predicted fragment length is 116 bps INFO @ Sun, 02 Jun 2019 17:19:13: #2 alternative fragment length(s) may be 95,101,116 bps INFO @ Sun, 02 Jun 2019 17:19:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX323680/SRX323680.20_model.r INFO @ Sun, 02 Jun 2019 17:19:13: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:19:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:19:17: 4000000 INFO @ Sun, 02 Jun 2019 17:19:19: #1 tag size is determined as 35 bps INFO @ Sun, 02 Jun 2019 17:19:19: #1 tag size = 35 INFO @ Sun, 02 Jun 2019 17:19:19: #1 total tags in treatment: 4762747 INFO @ Sun, 02 Jun 2019 17:19:19: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:19:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 17:19:19: #1 tags after filtering in treatment: 4762747 INFO @ Sun, 02 Jun 2019 17:19:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:19:19: #1 finished! INFO @ Sun, 02 Jun 2019 17:19:19: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:19:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:19:20: #2 number of paired peaks: 339 WARNING @ Sun, 02 Jun 2019 17:19:20: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Sun, 02 Jun 2019 17:19:20: start model_add_line... INFO @ Sun, 02 Jun 2019 17:19:20: start X-correlation... INFO @ Sun, 02 Jun 2019 17:19:20: end of X-cor INFO @ Sun, 02 Jun 2019 17:19:20: #2 finished! INFO @ Sun, 02 Jun 2019 17:19:20: #2 predicted fragment length is 116 bps INFO @ Sun, 02 Jun 2019 17:19:20: #2 alternative fragment length(s) may be 95,101,116 bps INFO @ Sun, 02 Jun 2019 17:19:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX323680/SRX323680.10_model.r INFO @ Sun, 02 Jun 2019 17:19:20: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:19:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:19:25: #1 tag size is determined as 35 bps INFO @ Sun, 02 Jun 2019 17:19:25: #1 tag size = 35 INFO @ Sun, 02 Jun 2019 17:19:25: #1 total tags in treatment: 4762747 INFO @ Sun, 02 Jun 2019 17:19:25: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:19:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 17:19:25: #1 tags after filtering in treatment: 4762747 INFO @ Sun, 02 Jun 2019 17:19:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:19:25: #1 finished! INFO @ Sun, 02 Jun 2019 17:19:25: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:19:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:19:26: #2 number of paired peaks: 339 WARNING @ Sun, 02 Jun 2019 17:19:26: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Sun, 02 Jun 2019 17:19:26: start model_add_line... INFO @ Sun, 02 Jun 2019 17:19:26: start X-correlation... INFO @ Sun, 02 Jun 2019 17:19:26: end of X-cor INFO @ Sun, 02 Jun 2019 17:19:26: #2 finished! INFO @ Sun, 02 Jun 2019 17:19:26: #2 predicted fragment length is 116 bps INFO @ Sun, 02 Jun 2019 17:19:26: #2 alternative fragment length(s) may be 95,101,116 bps INFO @ Sun, 02 Jun 2019 17:19:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX323680/SRX323680.05_model.r INFO @ Sun, 02 Jun 2019 17:19:26: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:19:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:19:28: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:19:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX323680/SRX323680.20_peaks.xls INFO @ Sun, 02 Jun 2019 17:19:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX323680/SRX323680.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:19:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX323680/SRX323680.20_summits.bed INFO @ Sun, 02 Jun 2019 17:19:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (148 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:19:35: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:19:41: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:19:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX323680/SRX323680.10_peaks.xls INFO @ Sun, 02 Jun 2019 17:19:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX323680/SRX323680.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:19:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX323680/SRX323680.10_summits.bed INFO @ Sun, 02 Jun 2019 17:19:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (288 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:19:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX323680/SRX323680.05_peaks.xls INFO @ Sun, 02 Jun 2019 17:19:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX323680/SRX323680.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:19:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX323680/SRX323680.05_summits.bed INFO @ Sun, 02 Jun 2019 17:19:48: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (489 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。