Job ID = 1291847 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,687,242 reads read : 13,687,242 reads written : 13,687,242 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: 00:02:54 13687242 reads; of these: 13687242 (100.00%) were unpaired; of these: 1770000 (12.93%) aligned 0 times 10029292 (73.27%) aligned exactly 1 time 1887950 (13.79%) aligned >1 times 87.07% overall alignment rate Time searching: 00:02:54 Overall time: 00:02:54 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] 6527734 / 11917242 = 0.5478 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 16:47:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257682/SRX257682.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257682/SRX257682.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257682/SRX257682.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257682/SRX257682.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 16:47:05: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:47:05: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:47:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257682/SRX257682.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257682/SRX257682.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257682/SRX257682.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257682/SRX257682.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 16:47:05: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:47:05: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:47:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257682/SRX257682.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257682/SRX257682.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257682/SRX257682.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257682/SRX257682.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 16:47:05: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:47:05: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:47:12: 1000000 INFO @ Sun, 02 Jun 2019 16:47:14: 1000000 INFO @ Sun, 02 Jun 2019 16:47:15: 1000000 INFO @ Sun, 02 Jun 2019 16:47:19: 2000000 INFO @ Sun, 02 Jun 2019 16:47:22: 2000000 INFO @ Sun, 02 Jun 2019 16:47:24: 2000000 INFO @ Sun, 02 Jun 2019 16:47:26: 3000000 INFO @ Sun, 02 Jun 2019 16:47:30: 3000000 INFO @ Sun, 02 Jun 2019 16:47:33: 3000000 INFO @ Sun, 02 Jun 2019 16:47:33: 4000000 INFO @ Sun, 02 Jun 2019 16:47:38: 4000000 INFO @ Sun, 02 Jun 2019 16:47:40: 5000000 INFO @ Sun, 02 Jun 2019 16:47:42: 4000000 INFO @ Sun, 02 Jun 2019 16:47:43: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 16:47:43: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 16:47:43: #1 total tags in treatment: 5389508 INFO @ Sun, 02 Jun 2019 16:47:43: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:47:43: #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 16:47:43: #1 tags after filtering in treatment: 5389508 INFO @ Sun, 02 Jun 2019 16:47:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:47:43: #1 finished! INFO @ Sun, 02 Jun 2019 16:47:43: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:47:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:47:44: #2 number of paired peaks: 713 WARNING @ Sun, 02 Jun 2019 16:47:44: Fewer paired peaks (713) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 713 pairs to build model! INFO @ Sun, 02 Jun 2019 16:47:44: start model_add_line... INFO @ Sun, 02 Jun 2019 16:47:44: start X-correlation... INFO @ Sun, 02 Jun 2019 16:47:44: end of X-cor INFO @ Sun, 02 Jun 2019 16:47:44: #2 finished! INFO @ Sun, 02 Jun 2019 16:47:44: #2 predicted fragment length is 123 bps INFO @ Sun, 02 Jun 2019 16:47:44: #2 alternative fragment length(s) may be 123 bps INFO @ Sun, 02 Jun 2019 16:47:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257682/SRX257682.05_model.r INFO @ Sun, 02 Jun 2019 16:47:44: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:47:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:47:46: 5000000 INFO @ Sun, 02 Jun 2019 16:47:49: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 16:47:49: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 16:47:49: #1 total tags in treatment: 5389508 INFO @ Sun, 02 Jun 2019 16:47:49: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:47:49: #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 16:47:50: #1 tags after filtering in treatment: 5389508 INFO @ Sun, 02 Jun 2019 16:47:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:47:50: #1 finished! INFO @ Sun, 02 Jun 2019 16:47:50: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:47:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:47:50: #2 number of paired peaks: 713 WARNING @ Sun, 02 Jun 2019 16:47:50: Fewer paired peaks (713) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 713 pairs to build model! INFO @ Sun, 02 Jun 2019 16:47:50: start model_add_line... INFO @ Sun, 02 Jun 2019 16:47:50: start X-correlation... INFO @ Sun, 02 Jun 2019 16:47:50: end of X-cor INFO @ Sun, 02 Jun 2019 16:47:50: #2 finished! INFO @ Sun, 02 Jun 2019 16:47:50: #2 predicted fragment length is 123 bps INFO @ Sun, 02 Jun 2019 16:47:50: #2 alternative fragment length(s) may be 123 bps INFO @ Sun, 02 Jun 2019 16:47:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257682/SRX257682.20_model.r INFO @ Sun, 02 Jun 2019 16:47:50: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:47:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:47:51: 5000000 INFO @ Sun, 02 Jun 2019 16:47:54: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 16:47:54: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 16:47:54: #1 total tags in treatment: 5389508 INFO @ Sun, 02 Jun 2019 16:47:54: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:47:54: #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 16:47:54: #1 tags after filtering in treatment: 5389508 INFO @ Sun, 02 Jun 2019 16:47:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:47:54: #1 finished! INFO @ Sun, 02 Jun 2019 16:47:54: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:47:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:47:55: #2 number of paired peaks: 713 WARNING @ Sun, 02 Jun 2019 16:47:55: Fewer paired peaks (713) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 713 pairs to build model! INFO @ Sun, 02 Jun 2019 16:47:55: start model_add_line... INFO @ Sun, 02 Jun 2019 16:47:55: start X-correlation... INFO @ Sun, 02 Jun 2019 16:47:55: end of X-cor INFO @ Sun, 02 Jun 2019 16:47:55: #2 finished! INFO @ Sun, 02 Jun 2019 16:47:55: #2 predicted fragment length is 123 bps INFO @ Sun, 02 Jun 2019 16:47:55: #2 alternative fragment length(s) may be 123 bps INFO @ Sun, 02 Jun 2019 16:47:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257682/SRX257682.10_model.r INFO @ Sun, 02 Jun 2019 16:47:55: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:47:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:48:01: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:48:07: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:48:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257682/SRX257682.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:48:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257682/SRX257682.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:48:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257682/SRX257682.05_summits.bed INFO @ Sun, 02 Jun 2019 16:48:09: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1579 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:48:12: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:48:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257682/SRX257682.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:48:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257682/SRX257682.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:48:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257682/SRX257682.20_summits.bed INFO @ Sun, 02 Jun 2019 16:48:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (341 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:48:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257682/SRX257682.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:48:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257682/SRX257682.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:48:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257682/SRX257682.10_summits.bed INFO @ Sun, 02 Jun 2019 16:48:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (807 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。