Job ID = 2589239 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,872,705 reads read : 2,872,705 reads written : 2,872,705 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR164270.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: 00:00:14 2872705 reads; of these: 2872705 (100.00%) were unpaired; of these: 2543185 (88.53%) aligned 0 times 290833 (10.12%) aligned exactly 1 time 38687 (1.35%) aligned >1 times 11.47% overall alignment rate Time searching: 00:00:14 Overall time: 00:00:14 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] 5696 / 329520 = 0.0173 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 17:12:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX054263/SRX054263.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX054263/SRX054263.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX054263/SRX054263.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX054263/SRX054263.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 17:12:49: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:12:49: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:12:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX054263/SRX054263.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX054263/SRX054263.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX054263/SRX054263.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX054263/SRX054263.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 17:12:50: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:12:50: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:12:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX054263/SRX054263.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX054263/SRX054263.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX054263/SRX054263.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX054263/SRX054263.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 17:12:51: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:12:51: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:12:51: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:12:51: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:12:51: #1 total tags in treatment: 323824 INFO @ Mon, 12 Aug 2019 17:12:51: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:12:51: #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 17:12:51: #1 tags after filtering in treatment: 323824 INFO @ Mon, 12 Aug 2019 17:12:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:12:51: #1 finished! INFO @ Mon, 12 Aug 2019 17:12:51: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:12:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:12:51: #2 number of paired peaks: 448 WARNING @ Mon, 12 Aug 2019 17:12:51: Fewer paired peaks (448) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 448 pairs to build model! INFO @ Mon, 12 Aug 2019 17:12:51: start model_add_line... INFO @ Mon, 12 Aug 2019 17:12:51: start X-correlation... INFO @ Mon, 12 Aug 2019 17:12:51: end of X-cor INFO @ Mon, 12 Aug 2019 17:12:51: #2 finished! INFO @ Mon, 12 Aug 2019 17:12:51: #2 predicted fragment length is 107 bps INFO @ Mon, 12 Aug 2019 17:12:51: #2 alternative fragment length(s) may be 107,179,201,546,587 bps INFO @ Mon, 12 Aug 2019 17:12:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX054263/SRX054263.05_model.r INFO @ Mon, 12 Aug 2019 17:12:51: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:12:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:12:52: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:12:52: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:12:52: #1 total tags in treatment: 323824 INFO @ Mon, 12 Aug 2019 17:12:52: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:12:52: #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 17:12:52: #1 tags after filtering in treatment: 323824 INFO @ Mon, 12 Aug 2019 17:12:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:12:52: #1 finished! INFO @ Mon, 12 Aug 2019 17:12:52: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:12:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:12:52: #2 number of paired peaks: 448 WARNING @ Mon, 12 Aug 2019 17:12:52: Fewer paired peaks (448) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 448 pairs to build model! INFO @ Mon, 12 Aug 2019 17:12:52: start model_add_line... INFO @ Mon, 12 Aug 2019 17:12:52: start X-correlation... INFO @ Mon, 12 Aug 2019 17:12:52: end of X-cor INFO @ Mon, 12 Aug 2019 17:12:52: #2 finished! INFO @ Mon, 12 Aug 2019 17:12:52: #2 predicted fragment length is 107 bps INFO @ Mon, 12 Aug 2019 17:12:52: #2 alternative fragment length(s) may be 107,179,201,546,587 bps INFO @ Mon, 12 Aug 2019 17:12:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX054263/SRX054263.10_model.r INFO @ Mon, 12 Aug 2019 17:12:52: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:12:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:12:52: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:12:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX054263/SRX054263.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:12:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX054263/SRX054263.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:12:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX054263/SRX054263.05_summits.bed INFO @ Mon, 12 Aug 2019 17:12:53: Done! INFO @ Mon, 12 Aug 2019 17:12:53: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:12:53: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:12:53: #1 total tags in treatment: 323824 INFO @ Mon, 12 Aug 2019 17:12:53: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:12:53: #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 17:12:53: #1 tags after filtering in treatment: 323824 INFO @ Mon, 12 Aug 2019 17:12:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:12:53: #1 finished! INFO @ Mon, 12 Aug 2019 17:12:53: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:12:53: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (10 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:12:53: #2 number of paired peaks: 448 WARNING @ Mon, 12 Aug 2019 17:12:53: Fewer paired peaks (448) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 448 pairs to build model! INFO @ Mon, 12 Aug 2019 17:12:53: start model_add_line... INFO @ Mon, 12 Aug 2019 17:12:53: start X-correlation... INFO @ Mon, 12 Aug 2019 17:12:53: end of X-cor INFO @ Mon, 12 Aug 2019 17:12:53: #2 finished! INFO @ Mon, 12 Aug 2019 17:12:53: #2 predicted fragment length is 107 bps INFO @ Mon, 12 Aug 2019 17:12:53: #2 alternative fragment length(s) may be 107,179,201,546,587 bps INFO @ Mon, 12 Aug 2019 17:12:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX054263/SRX054263.20_model.r INFO @ Mon, 12 Aug 2019 17:12:53: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:12:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:12:53: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 12 Aug 2019 17:12:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX054263/SRX054263.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:12:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX054263/SRX054263.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:12:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX054263/SRX054263.10_summits.bed INFO @ Mon, 12 Aug 2019 17:12:54: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (7 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:12:54: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 12 Aug 2019 17:12:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX054263/SRX054263.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:12:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX054263/SRX054263.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:12:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX054263/SRX054263.20_summits.bed INFO @ Mon, 12 Aug 2019 17:12:55: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis CompletedMACS2peakCalling