Job ID = 2010017 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 66,547 reads read : 66,547 reads written : 66,547 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR716607.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: 00:00:01 66547 reads; of these: 66547 (100.00%) were unpaired; of these: 14890 (22.38%) aligned 0 times 44028 (66.16%) aligned exactly 1 time 7629 (11.46%) aligned >1 times 77.62% overall alignment rate Time searching: 00:00:01 Overall time: 00:00:01 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] 42055 / 51657 = 0.8141 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 20:52:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX237126/SRX237126.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX237126/SRX237126.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX237126/SRX237126.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX237126/SRX237126.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 20:52:16: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:52:16: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:52:16: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 20:52:16: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 20:52:16: #1 total tags in treatment: 9602 INFO @ Fri, 05 Jul 2019 20:52:16: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:52:16: #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 20:52:16: #1 tags after filtering in treatment: 9601 INFO @ Fri, 05 Jul 2019 20:52:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 20:52:16: #1 finished! INFO @ Fri, 05 Jul 2019 20:52:16: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:52:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:52:16: #2 number of paired peaks: 400 WARNING @ Fri, 05 Jul 2019 20:52:16: Fewer paired peaks (400) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 400 pairs to build model! INFO @ Fri, 05 Jul 2019 20:52:16: start model_add_line... INFO @ Fri, 05 Jul 2019 20:52:16: start X-correlation... INFO @ Fri, 05 Jul 2019 20:52:16: end of X-cor INFO @ Fri, 05 Jul 2019 20:52:16: #2 finished! INFO @ Fri, 05 Jul 2019 20:52:16: #2 predicted fragment length is 291 bps INFO @ Fri, 05 Jul 2019 20:52:16: #2 alternative fragment length(s) may be 37,70,95,139,200,291,452,506,535,585 bps INFO @ Fri, 05 Jul 2019 20:52:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX237126/SRX237126.05_model.r INFO @ Fri, 05 Jul 2019 20:52:16: #3 Call peaks... INFO @ Fri, 05 Jul 2019 20:52:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 20:52:16: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 20:52:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX237126/SRX237126.05_peaks.xls INFO @ Fri, 05 Jul 2019 20:52:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX237126/SRX237126.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 20:52:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX237126/SRX237126.05_summits.bed INFO @ Fri, 05 Jul 2019 20:52:16: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 20:52:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX237126/SRX237126.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX237126/SRX237126.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX237126/SRX237126.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX237126/SRX237126.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 20:52:17: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:52:17: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:52:17: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 20:52:17: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 20:52:17: #1 total tags in treatment: 9602 INFO @ Fri, 05 Jul 2019 20:52:17: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:52:17: #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 20:52:17: #1 tags after filtering in treatment: 9601 INFO @ Fri, 05 Jul 2019 20:52:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 20:52:17: #1 finished! INFO @ Fri, 05 Jul 2019 20:52:17: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:52:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:52:17: #2 number of paired peaks: 400 WARNING @ Fri, 05 Jul 2019 20:52:17: Fewer paired peaks (400) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 400 pairs to build model! INFO @ Fri, 05 Jul 2019 20:52:17: start model_add_line... INFO @ Fri, 05 Jul 2019 20:52:17: start X-correlation... INFO @ Fri, 05 Jul 2019 20:52:17: end of X-cor INFO @ Fri, 05 Jul 2019 20:52:17: #2 finished! INFO @ Fri, 05 Jul 2019 20:52:17: #2 predicted fragment length is 291 bps INFO @ Fri, 05 Jul 2019 20:52:17: #2 alternative fragment length(s) may be 37,70,95,139,200,291,452,506,535,585 bps INFO @ Fri, 05 Jul 2019 20:52:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX237126/SRX237126.10_model.r INFO @ Fri, 05 Jul 2019 20:52:17: #3 Call peaks... INFO @ Fri, 05 Jul 2019 20:52:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 20:52:17: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 20:52:17: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX237126/SRX237126.10_peaks.xls INFO @ Fri, 05 Jul 2019 20:52:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX237126/SRX237126.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 20:52:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX237126/SRX237126.10_summits.bed INFO @ Fri, 05 Jul 2019 20:52:17: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) INFO @ Fri, 05 Jul 2019 20:52:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX237126/SRX237126.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX237126/SRX237126.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX237126/SRX237126.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX237126/SRX237126.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 20:52:18: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:52:18: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:52:18: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 20:52:18: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 20:52:18: #1 total tags in treatment: 9602 INFO @ Fri, 05 Jul 2019 20:52:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:52:18: #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 20:52:18: #1 tags after filtering in treatment: 9601 INFO @ Fri, 05 Jul 2019 20:52:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 20:52:18: #1 finished! INFO @ Fri, 05 Jul 2019 20:52:18: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:52:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:52:18: #2 number of paired peaks: 400 WARNING @ Fri, 05 Jul 2019 20:52:18: Fewer paired peaks (400) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 400 pairs to build model! INFO @ Fri, 05 Jul 2019 20:52:18: start model_add_line... INFO @ Fri, 05 Jul 2019 20:52:18: start X-correlation... INFO @ Fri, 05 Jul 2019 20:52:18: end of X-cor INFO @ Fri, 05 Jul 2019 20:52:18: #2 finished! INFO @ Fri, 05 Jul 2019 20:52:18: #2 predicted fragment length is 291 bps INFO @ Fri, 05 Jul 2019 20:52:18: #2 alternative fragment length(s) may be 37,70,95,139,200,291,452,506,535,585 bps INFO @ Fri, 05 Jul 2019 20:52:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX237126/SRX237126.20_model.r INFO @ Fri, 05 Jul 2019 20:52:18: #3 Call peaks... INFO @ Fri, 05 Jul 2019 20:52:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 20:52:18: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 20:52:18: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX237126/SRX237126.20_peaks.xls INFO @ Fri, 05 Jul 2019 20:52:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX237126/SRX237126.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 20:52:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX237126/SRX237126.20_summits.bed INFO @ Fri, 05 Jul 2019 20:52:18: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling CompletedMACS2peakCalling