Job ID = 2003761 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 923,047 reads read : 923,047 reads written : 923,047 rm: cannot remove ‘[DSE]RR*’: 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: 00:00:10 923047 reads; of these: 923047 (100.00%) were unpaired; of these: 648730 (70.28%) aligned 0 times 142020 (15.39%) aligned exactly 1 time 132297 (14.33%) aligned >1 times 29.72% overall alignment rate Time searching: 00:00:10 Overall time: 00:00:10 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] 124499 / 274317 = 0.4539 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 14:10:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX008703/ERX008703.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX008703/ERX008703.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX008703/ERX008703.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX008703/ERX008703.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 14:10:12: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:10:12: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:10:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX008703/ERX008703.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX008703/ERX008703.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX008703/ERX008703.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX008703/ERX008703.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 14:10:13: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:10:13: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:10:13: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 14:10:13: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 14:10:13: #1 total tags in treatment: 149818 INFO @ Fri, 05 Jul 2019 14:10:13: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:10:13: #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 14:10:13: #1 tags after filtering in treatment: 149818 INFO @ Fri, 05 Jul 2019 14:10:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:10:13: #1 finished! INFO @ Fri, 05 Jul 2019 14:10:13: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:10:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:10:13: #2 number of paired peaks: 171 WARNING @ Fri, 05 Jul 2019 14:10:13: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Fri, 05 Jul 2019 14:10:13: start model_add_line... INFO @ Fri, 05 Jul 2019 14:10:13: start X-correlation... INFO @ Fri, 05 Jul 2019 14:10:13: end of X-cor INFO @ Fri, 05 Jul 2019 14:10:13: #2 finished! INFO @ Fri, 05 Jul 2019 14:10:13: #2 predicted fragment length is 120 bps INFO @ Fri, 05 Jul 2019 14:10:13: #2 alternative fragment length(s) may be 120,541,545 bps INFO @ Fri, 05 Jul 2019 14:10:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX008703/ERX008703.05_model.r INFO @ Fri, 05 Jul 2019 14:10:13: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:10:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:10:14: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:10:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX008703/ERX008703.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX008703/ERX008703.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX008703/ERX008703.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX008703/ERX008703.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 14:10:14: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:10:14: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:10:14: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX008703/ERX008703.05_peaks.xls INFO @ Fri, 05 Jul 2019 14:10:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX008703/ERX008703.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:10:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX008703/ERX008703.05_summits.bed INFO @ Fri, 05 Jul 2019 14:10:14: Done! INFO @ Fri, 05 Jul 2019 14:10:14: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 14:10:14: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 14:10:14: #1 total tags in treatment: 149818 INFO @ Fri, 05 Jul 2019 14:10:14: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:10:14: #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 14:10:14: #1 tags after filtering in treatment: 149818 INFO @ Fri, 05 Jul 2019 14:10:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:10:14: #1 finished! INFO @ Fri, 05 Jul 2019 14:10:14: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:10:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:10:14: #2 number of paired peaks: 171 WARNING @ Fri, 05 Jul 2019 14:10:14: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Fri, 05 Jul 2019 14:10:14: start model_add_line... INFO @ Fri, 05 Jul 2019 14:10:14: start X-correlation... INFO @ Fri, 05 Jul 2019 14:10:14: end of X-cor INFO @ Fri, 05 Jul 2019 14:10:14: #2 finished! INFO @ Fri, 05 Jul 2019 14:10:14: #2 predicted fragment length is 120 bps INFO @ Fri, 05 Jul 2019 14:10:14: #2 alternative fragment length(s) may be 120,541,545 bps INFO @ Fri, 05 Jul 2019 14:10:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX008703/ERX008703.10_model.r INFO @ Fri, 05 Jul 2019 14:10:14: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:10:14: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (279 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 14:10:15: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 14:10:15: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX008703/ERX008703.10_peaks.xls INFO @ Fri, 05 Jul 2019 14:10:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX008703/ERX008703.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:10:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX008703/ERX008703.10_summits.bed INFO @ Fri, 05 Jul 2019 14:10:15: Done! INFO @ Fri, 05 Jul 2019 14:10:15: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 14:10:15: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 14:10:15: #1 total tags in treatment: 149818 INFO @ Fri, 05 Jul 2019 14:10:15: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:10:15: #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 14:10:15: #1 tags after filtering in treatment: 149818 INFO @ Fri, 05 Jul 2019 14:10:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:10:15: #1 finished! INFO @ Fri, 05 Jul 2019 14:10:15: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:10:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:10:15: #2 number of paired peaks: 171 WARNING @ Fri, 05 Jul 2019 14:10:15: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Fri, 05 Jul 2019 14:10:15: start model_add_line... INFO @ Fri, 05 Jul 2019 14:10:15: start X-correlation... INFO @ Fri, 05 Jul 2019 14:10:15: end of X-cor INFO @ Fri, 05 Jul 2019 14:10:15: #2 finished! INFO @ Fri, 05 Jul 2019 14:10:15: #2 predicted fragment length is 120 bps INFO @ Fri, 05 Jul 2019 14:10:15: #2 alternative fragment length(s) may be 120,541,545 bps INFO @ Fri, 05 Jul 2019 14:10:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX008703/ERX008703.20_model.r INFO @ Fri, 05 Jul 2019 14:10:15: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:10:15: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (128 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 14:10:16: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:10:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX008703/ERX008703.20_peaks.xls INFO @ Fri, 05 Jul 2019 14:10:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX008703/ERX008703.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:10:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX008703/ERX008703.20_summits.bed INFO @ Fri, 05 Jul 2019 14:10:16: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (61 records, 4 fields): 3 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BigWig に変換しました。 CompletedMACS2peakCalling