Job ID = 2009001 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,803,062 reads read : 1,803,062 reads written : 1,803,062 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR637580.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: 00:00:29 1803062 reads; of these: 1803062 (100.00%) were unpaired; of these: 78686 (4.36%) aligned 0 times 1430925 (79.36%) aligned exactly 1 time 293451 (16.28%) aligned >1 times 95.64% overall alignment rate Time searching: 00:00:29 Overall time: 00:00:29 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] 492813 / 1724376 = 0.2858 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 19:05:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594020/ERX594020.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594020/ERX594020.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594020/ERX594020.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594020/ERX594020.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 19:05:55: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:05:55: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:05:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594020/ERX594020.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594020/ERX594020.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594020/ERX594020.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594020/ERX594020.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 19:05:56: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:05:56: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:05:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594020/ERX594020.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594020/ERX594020.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594020/ERX594020.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594020/ERX594020.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 19:05:57: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:05:57: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:06:03: 1000000 INFO @ Fri, 05 Jul 2019 19:06:03: 1000000 INFO @ Fri, 05 Jul 2019 19:06:04: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 19:06:04: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 19:06:04: #1 total tags in treatment: 1231563 INFO @ Fri, 05 Jul 2019 19:06:04: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:06:04: #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 19:06:04: #1 tags after filtering in treatment: 1231563 INFO @ Fri, 05 Jul 2019 19:06:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:06:04: #1 finished! INFO @ Fri, 05 Jul 2019 19:06:04: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:06:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:06:05: #2 number of paired peaks: 535 WARNING @ Fri, 05 Jul 2019 19:06:05: Fewer paired peaks (535) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 535 pairs to build model! INFO @ Fri, 05 Jul 2019 19:06:05: start model_add_line... INFO @ Fri, 05 Jul 2019 19:06:05: start X-correlation... INFO @ Fri, 05 Jul 2019 19:06:05: end of X-cor INFO @ Fri, 05 Jul 2019 19:06:05: #2 finished! INFO @ Fri, 05 Jul 2019 19:06:05: #2 predicted fragment length is 138 bps INFO @ Fri, 05 Jul 2019 19:06:05: #2 alternative fragment length(s) may be 138 bps INFO @ Fri, 05 Jul 2019 19:06:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594020/ERX594020.10_model.r INFO @ Fri, 05 Jul 2019 19:06:05: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 19:06:05: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 19:06:05: #1 total tags in treatment: 1231563 INFO @ Fri, 05 Jul 2019 19:06:05: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:06:05: #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 19:06:05: #1 tags after filtering in treatment: 1231563 INFO @ Fri, 05 Jul 2019 19:06:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:06:05: #1 finished! INFO @ Fri, 05 Jul 2019 19:06:05: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:06:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:06:05: #2 number of paired peaks: 535 WARNING @ Fri, 05 Jul 2019 19:06:05: Fewer paired peaks (535) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 535 pairs to build model! INFO @ Fri, 05 Jul 2019 19:06:05: start model_add_line... INFO @ Fri, 05 Jul 2019 19:06:05: start X-correlation... INFO @ Fri, 05 Jul 2019 19:06:05: end of X-cor INFO @ Fri, 05 Jul 2019 19:06:05: #2 finished! INFO @ Fri, 05 Jul 2019 19:06:05: #2 predicted fragment length is 138 bps INFO @ Fri, 05 Jul 2019 19:06:05: #2 alternative fragment length(s) may be 138 bps INFO @ Fri, 05 Jul 2019 19:06:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594020/ERX594020.05_model.r INFO @ Fri, 05 Jul 2019 19:06:05: 1000000 INFO @ Fri, 05 Jul 2019 19:06:07: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 19:06:07: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 19:06:07: #1 total tags in treatment: 1231563 INFO @ Fri, 05 Jul 2019 19:06:07: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:06:07: #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 19:06:07: #1 tags after filtering in treatment: 1231563 INFO @ Fri, 05 Jul 2019 19:06:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:06:07: #1 finished! INFO @ Fri, 05 Jul 2019 19:06:07: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:06:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:06:07: #2 number of paired peaks: 535 WARNING @ Fri, 05 Jul 2019 19:06:07: Fewer paired peaks (535) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 535 pairs to build model! INFO @ Fri, 05 Jul 2019 19:06:07: start model_add_line... INFO @ Fri, 05 Jul 2019 19:06:07: start X-correlation... INFO @ Fri, 05 Jul 2019 19:06:07: end of X-cor INFO @ Fri, 05 Jul 2019 19:06:07: #2 finished! INFO @ Fri, 05 Jul 2019 19:06:07: #2 predicted fragment length is 138 bps INFO @ Fri, 05 Jul 2019 19:06:07: #2 alternative fragment length(s) may be 138 bps INFO @ Fri, 05 Jul 2019 19:06:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594020/ERX594020.20_model.r BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 19:06:34: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:06:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:06:34: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:06:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:06:34: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:06:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:06:39: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:06:39: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:06:39: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:06:41: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594020/ERX594020.10_peaks.xls INFO @ Fri, 05 Jul 2019 19:06:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594020/ERX594020.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:06:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594020/ERX594020.10_summits.bed INFO @ Fri, 05 Jul 2019 19:06:41: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594020/ERX594020.05_peaks.xls INFO @ Fri, 05 Jul 2019 19:06:41: Done! INFO @ Fri, 05 Jul 2019 19:06:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594020/ERX594020.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:06:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594020/ERX594020.05_summits.bed INFO @ Fri, 05 Jul 2019 19:06:41: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (1999 records, 4 fields): 7 millis pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (3014 records, 4 fields): 9 millis INFO @ Fri, 05 Jul 2019 19:06:41: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594020/ERX594020.20_peaks.xls INFO @ Fri, 05 Jul 2019 19:06:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594020/ERX594020.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:06:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594020/ERX594020.20_summits.bed INFO @ Fri, 05 Jul 2019 19:06:41: Done! BigWig に変換しました。 pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (1070 records, 4 fields): 5 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling