Job ID = 2589175 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,849,260 reads read : 4,849,260 reads written : 4,849,260 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR107557.sra.cache’: 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: 00:00:52 4849260 reads; of these: 4849260 (100.00%) were unpaired; of these: 1357780 (28.00%) aligned 0 times 2964252 (61.13%) aligned exactly 1 time 527228 (10.87%) aligned >1 times 72.00% overall alignment rate Time searching: 00:00:52 Overall time: 00:00:52 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] 717703 / 3491480 = 0.2056 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 17:05:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043982/SRX043982.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043982/SRX043982.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043982/SRX043982.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043982/SRX043982.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 17:05:31: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:05:31: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:05:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043982/SRX043982.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043982/SRX043982.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043982/SRX043982.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043982/SRX043982.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 17:05:31: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:05:31: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:05:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043982/SRX043982.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043982/SRX043982.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043982/SRX043982.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043982/SRX043982.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 17:05:32: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:05:32: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:05:38: 1000000 INFO @ Mon, 12 Aug 2019 17:05:39: 1000000 INFO @ Mon, 12 Aug 2019 17:05:40: 1000000 INFO @ Mon, 12 Aug 2019 17:05:46: 2000000 INFO @ Mon, 12 Aug 2019 17:05:46: 2000000 INFO @ Mon, 12 Aug 2019 17:05:49: 2000000 INFO @ Mon, 12 Aug 2019 17:05:52: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:05:52: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:05:52: #1 total tags in treatment: 2773777 INFO @ Mon, 12 Aug 2019 17:05:52: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:05:52: #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 17:05:52: #1 tags after filtering in treatment: 2773777 INFO @ Mon, 12 Aug 2019 17:05:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:05:52: #1 finished! INFO @ Mon, 12 Aug 2019 17:05:52: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:05:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:05:52: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:05:52: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:05:52: #1 total tags in treatment: 2773777 INFO @ Mon, 12 Aug 2019 17:05:52: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:05:52: #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 17:05:52: #1 tags after filtering in treatment: 2773777 INFO @ Mon, 12 Aug 2019 17:05:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:05:52: #1 finished! INFO @ Mon, 12 Aug 2019 17:05:52: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:05:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:05:52: #2 number of paired peaks: 688 WARNING @ Mon, 12 Aug 2019 17:05:52: Fewer paired peaks (688) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 688 pairs to build model! INFO @ Mon, 12 Aug 2019 17:05:52: start model_add_line... INFO @ Mon, 12 Aug 2019 17:05:52: start X-correlation... INFO @ Mon, 12 Aug 2019 17:05:52: end of X-cor INFO @ Mon, 12 Aug 2019 17:05:52: #2 finished! INFO @ Mon, 12 Aug 2019 17:05:52: #2 predicted fragment length is 129 bps INFO @ Mon, 12 Aug 2019 17:05:52: #2 alternative fragment length(s) may be 129 bps INFO @ Mon, 12 Aug 2019 17:05:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043982/SRX043982.05_model.r INFO @ Mon, 12 Aug 2019 17:05:52: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:05:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:05:52: #2 number of paired peaks: 688 WARNING @ Mon, 12 Aug 2019 17:05:52: Fewer paired peaks (688) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 688 pairs to build model! INFO @ Mon, 12 Aug 2019 17:05:52: start model_add_line... INFO @ Mon, 12 Aug 2019 17:05:52: start X-correlation... INFO @ Mon, 12 Aug 2019 17:05:52: end of X-cor INFO @ Mon, 12 Aug 2019 17:05:52: #2 finished! INFO @ Mon, 12 Aug 2019 17:05:52: #2 predicted fragment length is 129 bps INFO @ Mon, 12 Aug 2019 17:05:52: #2 alternative fragment length(s) may be 129 bps INFO @ Mon, 12 Aug 2019 17:05:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043982/SRX043982.10_model.r INFO @ Mon, 12 Aug 2019 17:05:52: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:05:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:05:55: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:05:55: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:05:55: #1 total tags in treatment: 2773777 INFO @ Mon, 12 Aug 2019 17:05:55: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:05:55: #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 17:05:56: #1 tags after filtering in treatment: 2773777 INFO @ Mon, 12 Aug 2019 17:05:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:05:56: #1 finished! INFO @ Mon, 12 Aug 2019 17:05:56: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:05:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:05:56: #2 number of paired peaks: 688 WARNING @ Mon, 12 Aug 2019 17:05:56: Fewer paired peaks (688) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 688 pairs to build model! INFO @ Mon, 12 Aug 2019 17:05:56: start model_add_line... INFO @ Mon, 12 Aug 2019 17:05:56: start X-correlation... INFO @ Mon, 12 Aug 2019 17:05:56: end of X-cor INFO @ Mon, 12 Aug 2019 17:05:56: #2 finished! INFO @ Mon, 12 Aug 2019 17:05:56: #2 predicted fragment length is 129 bps INFO @ Mon, 12 Aug 2019 17:05:56: #2 alternative fragment length(s) may be 129 bps INFO @ Mon, 12 Aug 2019 17:05:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043982/SRX043982.20_model.r INFO @ Mon, 12 Aug 2019 17:05:56: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:05:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:06:01: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:06:01: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:06:05: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:06:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043982/SRX043982.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:06:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043982/SRX043982.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:06:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043982/SRX043982.05_summits.bed INFO @ Mon, 12 Aug 2019 17:06:05: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (2500 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:06:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043982/SRX043982.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:06:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043982/SRX043982.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:06:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043982/SRX043982.10_summits.bed INFO @ Mon, 12 Aug 2019 17:06:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1108 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:06:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043982/SRX043982.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:06:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043982/SRX043982.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:06:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043982/SRX043982.20_summits.bed INFO @ Mon, 12 Aug 2019 17:06:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (307 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。