Job ID = 1292032 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,892,613 reads read : 7,892,613 reads written : 7,892,613 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: 00:02:18 7892613 reads; of these: 7892613 (100.00%) were unpaired; of these: 2115017 (26.80%) aligned 0 times 4907133 (62.17%) aligned exactly 1 time 870463 (11.03%) aligned >1 times 73.20% overall alignment rate Time searching: 00:02:18 Overall time: 00:02:18 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] 1608311 / 5777596 = 0.2784 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 17:18:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX323678/SRX323678.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX323678/SRX323678.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX323678/SRX323678.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX323678/SRX323678.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 17:18:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX323678/SRX323678.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX323678/SRX323678.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX323678/SRX323678.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX323678/SRX323678.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 17:18:41: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:18:41: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:18:41: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:18:41: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:18:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX323678/SRX323678.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX323678/SRX323678.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX323678/SRX323678.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX323678/SRX323678.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 17:18:41: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:18:41: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:18:50: 1000000 INFO @ Sun, 02 Jun 2019 17:18:53: 1000000 INFO @ Sun, 02 Jun 2019 17:18:53: 1000000 INFO @ Sun, 02 Jun 2019 17:18:59: 2000000 INFO @ Sun, 02 Jun 2019 17:19:04: 2000000 INFO @ Sun, 02 Jun 2019 17:19:04: 2000000 INFO @ Sun, 02 Jun 2019 17:19:08: 3000000 INFO @ Sun, 02 Jun 2019 17:19:16: 3000000 INFO @ Sun, 02 Jun 2019 17:19:16: 3000000 INFO @ Sun, 02 Jun 2019 17:19:17: 4000000 INFO @ Sun, 02 Jun 2019 17:19:18: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 17:19:18: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 17:19:18: #1 total tags in treatment: 4169285 INFO @ Sun, 02 Jun 2019 17:19:18: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:19:18: #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 17:19:18: #1 tags after filtering in treatment: 4169285 INFO @ Sun, 02 Jun 2019 17:19:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:19:18: #1 finished! INFO @ Sun, 02 Jun 2019 17:19:18: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:19:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:19:19: #2 number of paired peaks: 212 WARNING @ Sun, 02 Jun 2019 17:19:19: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Sun, 02 Jun 2019 17:19:19: start model_add_line... INFO @ Sun, 02 Jun 2019 17:19:19: start X-correlation... INFO @ Sun, 02 Jun 2019 17:19:19: end of X-cor INFO @ Sun, 02 Jun 2019 17:19:19: #2 finished! INFO @ Sun, 02 Jun 2019 17:19:19: #2 predicted fragment length is 164 bps INFO @ Sun, 02 Jun 2019 17:19:19: #2 alternative fragment length(s) may be 164,591,598 bps INFO @ Sun, 02 Jun 2019 17:19:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX323678/SRX323678.10_model.r INFO @ Sun, 02 Jun 2019 17:19:19: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:19:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:19:28: 4000000 INFO @ Sun, 02 Jun 2019 17:19:28: 4000000 INFO @ Sun, 02 Jun 2019 17:19:30: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 17:19:30: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 17:19:30: #1 total tags in treatment: 4169285 INFO @ Sun, 02 Jun 2019 17:19:30: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:19:30: #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 17:19:30: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 17:19:30: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 17:19:30: #1 total tags in treatment: 4169285 INFO @ Sun, 02 Jun 2019 17:19:30: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:19:30: #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 17:19:30: #1 tags after filtering in treatment: 4169285 INFO @ Sun, 02 Jun 2019 17:19:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:19:30: #1 finished! INFO @ Sun, 02 Jun 2019 17:19:30: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:19:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:19:30: #1 tags after filtering in treatment: 4169285 INFO @ Sun, 02 Jun 2019 17:19:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:19:30: #1 finished! INFO @ Sun, 02 Jun 2019 17:19:30: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:19:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:19:30: #2 number of paired peaks: 212 WARNING @ Sun, 02 Jun 2019 17:19:30: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Sun, 02 Jun 2019 17:19:30: start model_add_line... INFO @ Sun, 02 Jun 2019 17:19:30: #2 number of paired peaks: 212 WARNING @ Sun, 02 Jun 2019 17:19:30: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Sun, 02 Jun 2019 17:19:30: start model_add_line... INFO @ Sun, 02 Jun 2019 17:19:30: start X-correlation... INFO @ Sun, 02 Jun 2019 17:19:30: start X-correlation... INFO @ Sun, 02 Jun 2019 17:19:30: end of X-cor INFO @ Sun, 02 Jun 2019 17:19:30: #2 finished! INFO @ Sun, 02 Jun 2019 17:19:30: #2 predicted fragment length is 164 bps INFO @ Sun, 02 Jun 2019 17:19:30: #2 alternative fragment length(s) may be 164,591,598 bps INFO @ Sun, 02 Jun 2019 17:19:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX323678/SRX323678.20_model.r INFO @ Sun, 02 Jun 2019 17:19:30: end of X-cor INFO @ Sun, 02 Jun 2019 17:19:30: #2 finished! INFO @ Sun, 02 Jun 2019 17:19:30: #2 predicted fragment length is 164 bps INFO @ Sun, 02 Jun 2019 17:19:30: #2 alternative fragment length(s) may be 164,591,598 bps INFO @ Sun, 02 Jun 2019 17:19:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX323678/SRX323678.05_model.r INFO @ Sun, 02 Jun 2019 17:19:30: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:19:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:19:30: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:19:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:19:31: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:19:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX323678/SRX323678.10_peaks.xls INFO @ Sun, 02 Jun 2019 17:19:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX323678/SRX323678.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:19:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX323678/SRX323678.10_summits.bed INFO @ Sun, 02 Jun 2019 17:19:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (185 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:19:42: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:19:43: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:19:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX323678/SRX323678.20_peaks.xls INFO @ Sun, 02 Jun 2019 17:19:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX323678/SRX323678.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:19:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX323678/SRX323678.20_summits.bed INFO @ Sun, 02 Jun 2019 17:19:49: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (74 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:19:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX323678/SRX323678.05_peaks.xls INFO @ Sun, 02 Jun 2019 17:19:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX323678/SRX323678.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:19:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX323678/SRX323678.05_summits.bed INFO @ Sun, 02 Jun 2019 17:19:49: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (335 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。