Job ID = 2590030 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,698,930 reads read : 17,698,930 reads written : 17,698,930 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: 00:02:28 17698930 reads; of these: 17698930 (100.00%) were unpaired; of these: 8433410 (47.65%) aligned 0 times 7955799 (44.95%) aligned exactly 1 time 1309721 (7.40%) aligned >1 times 52.35% overall alignment rate Time searching: 00:02:28 Overall time: 00:02:28 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] 4767152 / 9265520 = 0.5145 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 19:25:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494874/SRX494874.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494874/SRX494874.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494874/SRX494874.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494874/SRX494874.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 @ Mon, 12 Aug 2019 19:25:03: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:25:03: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:25:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494874/SRX494874.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494874/SRX494874.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494874/SRX494874.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494874/SRX494874.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 @ Mon, 12 Aug 2019 19:25:04: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:25:04: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:25:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494874/SRX494874.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494874/SRX494874.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494874/SRX494874.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494874/SRX494874.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 @ Mon, 12 Aug 2019 19:25:05: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:25:05: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:25:10: 1000000 INFO @ Mon, 12 Aug 2019 19:25:11: 1000000 INFO @ Mon, 12 Aug 2019 19:25:12: 1000000 INFO @ Mon, 12 Aug 2019 19:25:17: 2000000 INFO @ Mon, 12 Aug 2019 19:25:19: 2000000 INFO @ Mon, 12 Aug 2019 19:25:19: 2000000 INFO @ Mon, 12 Aug 2019 19:25:24: 3000000 INFO @ Mon, 12 Aug 2019 19:25:26: 3000000 INFO @ Mon, 12 Aug 2019 19:25:26: 3000000 INFO @ Mon, 12 Aug 2019 19:25:30: 4000000 INFO @ Mon, 12 Aug 2019 19:25:32: 4000000 INFO @ Mon, 12 Aug 2019 19:25:34: 4000000 INFO @ Mon, 12 Aug 2019 19:25:34: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:25:34: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:25:34: #1 total tags in treatment: 4498368 INFO @ Mon, 12 Aug 2019 19:25:34: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:25:34: #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 19:25:34: #1 tags after filtering in treatment: 4498368 INFO @ Mon, 12 Aug 2019 19:25:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:25:34: #1 finished! INFO @ Mon, 12 Aug 2019 19:25:34: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:25:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:25:34: #2 number of paired peaks: 693 WARNING @ Mon, 12 Aug 2019 19:25:34: Fewer paired peaks (693) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 693 pairs to build model! INFO @ Mon, 12 Aug 2019 19:25:34: start model_add_line... INFO @ Mon, 12 Aug 2019 19:25:34: start X-correlation... INFO @ Mon, 12 Aug 2019 19:25:34: end of X-cor INFO @ Mon, 12 Aug 2019 19:25:34: #2 finished! INFO @ Mon, 12 Aug 2019 19:25:34: #2 predicted fragment length is 128 bps INFO @ Mon, 12 Aug 2019 19:25:34: #2 alternative fragment length(s) may be 128 bps INFO @ Mon, 12 Aug 2019 19:25:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494874/SRX494874.05_model.r INFO @ Mon, 12 Aug 2019 19:25:34: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:25:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:25:36: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:25:36: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:25:36: #1 total tags in treatment: 4498368 INFO @ Mon, 12 Aug 2019 19:25:36: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:25:36: #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 19:25:36: #1 tags after filtering in treatment: 4498368 INFO @ Mon, 12 Aug 2019 19:25:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:25:36: #1 finished! INFO @ Mon, 12 Aug 2019 19:25:36: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:25:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:25:36: #2 number of paired peaks: 693 WARNING @ Mon, 12 Aug 2019 19:25:36: Fewer paired peaks (693) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 693 pairs to build model! INFO @ Mon, 12 Aug 2019 19:25:36: start model_add_line... INFO @ Mon, 12 Aug 2019 19:25:36: start X-correlation... INFO @ Mon, 12 Aug 2019 19:25:36: end of X-cor INFO @ Mon, 12 Aug 2019 19:25:36: #2 finished! INFO @ Mon, 12 Aug 2019 19:25:36: #2 predicted fragment length is 128 bps INFO @ Mon, 12 Aug 2019 19:25:36: #2 alternative fragment length(s) may be 128 bps INFO @ Mon, 12 Aug 2019 19:25:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494874/SRX494874.20_model.r INFO @ Mon, 12 Aug 2019 19:25:36: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:25:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:25:37: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:25:37: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:25:37: #1 total tags in treatment: 4498368 INFO @ Mon, 12 Aug 2019 19:25:37: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:25:37: #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 19:25:37: #1 tags after filtering in treatment: 4498368 INFO @ Mon, 12 Aug 2019 19:25:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:25:37: #1 finished! INFO @ Mon, 12 Aug 2019 19:25:37: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:25:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:25:38: #2 number of paired peaks: 693 WARNING @ Mon, 12 Aug 2019 19:25:38: Fewer paired peaks (693) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 693 pairs to build model! INFO @ Mon, 12 Aug 2019 19:25:38: start model_add_line... INFO @ Mon, 12 Aug 2019 19:25:38: start X-correlation... INFO @ Mon, 12 Aug 2019 19:25:38: end of X-cor INFO @ Mon, 12 Aug 2019 19:25:38: #2 finished! INFO @ Mon, 12 Aug 2019 19:25:38: #2 predicted fragment length is 128 bps INFO @ Mon, 12 Aug 2019 19:25:38: #2 alternative fragment length(s) may be 128 bps INFO @ Mon, 12 Aug 2019 19:25:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494874/SRX494874.10_model.r INFO @ Mon, 12 Aug 2019 19:25:38: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:25:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:25:49: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:25:51: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:25:52: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:25:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494874/SRX494874.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:25:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494874/SRX494874.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:25:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494874/SRX494874.05_summits.bed INFO @ Mon, 12 Aug 2019 19:25:55: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (872 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:25:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494874/SRX494874.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:25:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494874/SRX494874.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:25:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494874/SRX494874.20_summits.bed INFO @ Mon, 12 Aug 2019 19:25:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (233 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:25:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494874/SRX494874.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:25:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494874/SRX494874.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:25:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494874/SRX494874.10_summits.bed INFO @ Mon, 12 Aug 2019 19:25:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (464 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。