Job ID = 2007226 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 721,029 reads read : 721,029 reads written : 721,029 spots read : 693,214 reads read : 693,214 reads written : 693,214 spots read : 703,309 reads read : 703,309 reads written : 703,309 spots read : 691,314 reads read : 691,314 reads written : 691,314 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529626.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529627.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: 00:00:45 2808866 reads; of these: 2808866 (100.00%) were unpaired; of these: 95539 (3.40%) aligned 0 times 2296680 (81.77%) aligned exactly 1 time 416647 (14.83%) aligned >1 times 96.60% overall alignment rate Time searching: 00:00:45 Overall time: 00:00:45 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdupse_core] 2582489 / 2713327 = 0.9518 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 @ Fri, 05 Jul 2019 15:50:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548196/ERX2548196.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548196/ERX2548196.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548196/ERX2548196.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548196/ERX2548196.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 05 Jul 2019 15:50:31: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:50:31: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:50:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548196/ERX2548196.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548196/ERX2548196.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548196/ERX2548196.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548196/ERX2548196.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 05 Jul 2019 15:50:32: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:50:32: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:50:32: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:50:32: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:50:32: #1 total tags in treatment: 130838 INFO @ Fri, 05 Jul 2019 15:50:32: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:50:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 15:50:32: #1 tags after filtering in treatment: 130838 INFO @ Fri, 05 Jul 2019 15:50:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:50:32: #1 finished! INFO @ Fri, 05 Jul 2019 15:50:32: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:50:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:50:32: #2 number of paired peaks: 376 WARNING @ Fri, 05 Jul 2019 15:50:32: Fewer paired peaks (376) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 376 pairs to build model! INFO @ Fri, 05 Jul 2019 15:50:32: start model_add_line... INFO @ Fri, 05 Jul 2019 15:50:32: start X-correlation... INFO @ Fri, 05 Jul 2019 15:50:32: end of X-cor INFO @ Fri, 05 Jul 2019 15:50:32: #2 finished! INFO @ Fri, 05 Jul 2019 15:50:32: #2 predicted fragment length is 185 bps INFO @ Fri, 05 Jul 2019 15:50:32: #2 alternative fragment length(s) may be 4,40,135,185,211,230,276,316,358,502,537,582 bps INFO @ Fri, 05 Jul 2019 15:50:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548196/ERX2548196.05_model.r INFO @ Fri, 05 Jul 2019 15:50:32: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:50:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:50:33: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:50:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548196/ERX2548196.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548196/ERX2548196.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548196/ERX2548196.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548196/ERX2548196.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 05 Jul 2019 15:50:33: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:50:33: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:50:33: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548196/ERX2548196.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:50:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548196/ERX2548196.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:50:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548196/ERX2548196.05_summits.bed INFO @ Fri, 05 Jul 2019 15:50:33: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (19 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 15:50:33: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:50:33: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:50:33: #1 total tags in treatment: 130838 INFO @ Fri, 05 Jul 2019 15:50:33: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:50:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 15:50:33: #1 tags after filtering in treatment: 130838 INFO @ Fri, 05 Jul 2019 15:50:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:50:33: #1 finished! INFO @ Fri, 05 Jul 2019 15:50:33: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:50:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:50:33: #2 number of paired peaks: 376 WARNING @ Fri, 05 Jul 2019 15:50:33: Fewer paired peaks (376) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 376 pairs to build model! INFO @ Fri, 05 Jul 2019 15:50:33: start model_add_line... INFO @ Fri, 05 Jul 2019 15:50:33: start X-correlation... INFO @ Fri, 05 Jul 2019 15:50:33: end of X-cor INFO @ Fri, 05 Jul 2019 15:50:33: #2 finished! INFO @ Fri, 05 Jul 2019 15:50:33: #2 predicted fragment length is 185 bps INFO @ Fri, 05 Jul 2019 15:50:33: #2 alternative fragment length(s) may be 4,40,135,185,211,230,276,316,358,502,537,582 bps INFO @ Fri, 05 Jul 2019 15:50:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548196/ERX2548196.10_model.r INFO @ Fri, 05 Jul 2019 15:50:33: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:50:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 15:50:34: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:50:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548196/ERX2548196.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:50:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548196/ERX2548196.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:50:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548196/ERX2548196.10_summits.bed INFO @ Fri, 05 Jul 2019 15:50:34: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (2 records, 4 fields): 1 millis INFO @ Fri, 05 Jul 2019 15:50:34: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:50:34: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:50:34: #1 total tags in treatment: 130838 INFO @ Fri, 05 Jul 2019 15:50:34: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:50:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 15:50:34: #1 tags after filtering in treatment: 130838 INFO @ Fri, 05 Jul 2019 15:50:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:50:34: #1 finished! INFO @ Fri, 05 Jul 2019 15:50:34: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:50:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:50:34: #2 number of paired peaks: 376 WARNING @ Fri, 05 Jul 2019 15:50:34: Fewer paired peaks (376) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 376 pairs to build model! INFO @ Fri, 05 Jul 2019 15:50:34: start model_add_line... INFO @ Fri, 05 Jul 2019 15:50:34: start X-correlation... INFO @ Fri, 05 Jul 2019 15:50:34: end of X-cor INFO @ Fri, 05 Jul 2019 15:50:34: #2 finished! INFO @ Fri, 05 Jul 2019 15:50:34: #2 predicted fragment length is 185 bps INFO @ Fri, 05 Jul 2019 15:50:34: #2 alternative fragment length(s) may be 4,40,135,185,211,230,276,316,358,502,537,582 bps INFO @ Fri, 05 Jul 2019 15:50:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548196/ERX2548196.20_model.r INFO @ Fri, 05 Jul 2019 15:50:34: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:50:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:50:35: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:50:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548196/ERX2548196.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:50:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548196/ERX2548196.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:50:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548196/ERX2548196.20_summits.bed INFO @ Fri, 05 Jul 2019 15:50:35: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling