Job ID = 2009756 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,410,222 reads read : 3,410,222 reads written : 3,410,222 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR497933.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: 00:01:31 3410222 reads; of these: 3410222 (100.00%) were unpaired; of these: 1279903 (37.53%) aligned 0 times 1669047 (48.94%) aligned exactly 1 time 461272 (13.53%) aligned >1 times 62.47% overall alignment rate Time searching: 00:01:31 Overall time: 00:01:31 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] 812731 / 2130319 = 0.3815 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 19:47:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX148612/SRX148612.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX148612/SRX148612.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX148612/SRX148612.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX148612/SRX148612.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 19:47:28: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:47:28: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:47:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX148612/SRX148612.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX148612/SRX148612.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX148612/SRX148612.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX148612/SRX148612.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 19:47:29: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:47:29: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:47:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX148612/SRX148612.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX148612/SRX148612.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX148612/SRX148612.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX148612/SRX148612.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 19:47:30: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:47:30: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:47:36: 1000000 INFO @ Fri, 05 Jul 2019 19:47:38: 1000000 INFO @ Fri, 05 Jul 2019 19:47:39: #1 tag size is determined as 30 bps INFO @ Fri, 05 Jul 2019 19:47:39: #1 tag size = 30 INFO @ Fri, 05 Jul 2019 19:47:39: #1 total tags in treatment: 1317588 INFO @ Fri, 05 Jul 2019 19:47:39: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:47:39: #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 19:47:39: #1 tags after filtering in treatment: 1317588 INFO @ Fri, 05 Jul 2019 19:47:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:47:39: #1 finished! INFO @ Fri, 05 Jul 2019 19:47:39: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:47:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:47:39: #2 number of paired peaks: 135 WARNING @ Fri, 05 Jul 2019 19:47:39: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Fri, 05 Jul 2019 19:47:39: start model_add_line... INFO @ Fri, 05 Jul 2019 19:47:39: start X-correlation... INFO @ Fri, 05 Jul 2019 19:47:39: end of X-cor INFO @ Fri, 05 Jul 2019 19:47:39: #2 finished! INFO @ Fri, 05 Jul 2019 19:47:39: #2 predicted fragment length is 194 bps INFO @ Fri, 05 Jul 2019 19:47:39: #2 alternative fragment length(s) may be 4,194,217 bps INFO @ Fri, 05 Jul 2019 19:47:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX148612/SRX148612.05_model.r INFO @ Fri, 05 Jul 2019 19:47:39: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:47:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:47:39: 1000000 INFO @ Fri, 05 Jul 2019 19:47:41: #1 tag size is determined as 30 bps INFO @ Fri, 05 Jul 2019 19:47:41: #1 tag size = 30 INFO @ Fri, 05 Jul 2019 19:47:41: #1 total tags in treatment: 1317588 INFO @ Fri, 05 Jul 2019 19:47:41: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:47:41: #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 19:47:41: #1 tags after filtering in treatment: 1317588 INFO @ Fri, 05 Jul 2019 19:47:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:47:41: #1 finished! INFO @ Fri, 05 Jul 2019 19:47:41: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:47:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:47:41: #2 number of paired peaks: 135 WARNING @ Fri, 05 Jul 2019 19:47:41: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Fri, 05 Jul 2019 19:47:41: start model_add_line... INFO @ Fri, 05 Jul 2019 19:47:41: start X-correlation... INFO @ Fri, 05 Jul 2019 19:47:41: end of X-cor INFO @ Fri, 05 Jul 2019 19:47:41: #2 finished! INFO @ Fri, 05 Jul 2019 19:47:41: #2 predicted fragment length is 194 bps INFO @ Fri, 05 Jul 2019 19:47:41: #2 alternative fragment length(s) may be 4,194,217 bps INFO @ Fri, 05 Jul 2019 19:47:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX148612/SRX148612.10_model.r INFO @ Fri, 05 Jul 2019 19:47:41: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:47:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:47:42: #1 tag size is determined as 30 bps INFO @ Fri, 05 Jul 2019 19:47:42: #1 tag size = 30 INFO @ Fri, 05 Jul 2019 19:47:42: #1 total tags in treatment: 1317588 INFO @ Fri, 05 Jul 2019 19:47:42: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:47:42: #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 19:47:42: #1 tags after filtering in treatment: 1317588 INFO @ Fri, 05 Jul 2019 19:47:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:47:42: #1 finished! INFO @ Fri, 05 Jul 2019 19:47:42: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:47:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:47:42: #2 number of paired peaks: 135 WARNING @ Fri, 05 Jul 2019 19:47:42: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Fri, 05 Jul 2019 19:47:42: start model_add_line... INFO @ Fri, 05 Jul 2019 19:47:42: start X-correlation... INFO @ Fri, 05 Jul 2019 19:47:42: end of X-cor INFO @ Fri, 05 Jul 2019 19:47:42: #2 finished! INFO @ Fri, 05 Jul 2019 19:47:42: #2 predicted fragment length is 194 bps INFO @ Fri, 05 Jul 2019 19:47:42: #2 alternative fragment length(s) may be 4,194,217 bps INFO @ Fri, 05 Jul 2019 19:47:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX148612/SRX148612.20_model.r INFO @ Fri, 05 Jul 2019 19:47:42: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:47:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:47:45: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:47:47: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX148612/SRX148612.05_peaks.xls INFO @ Fri, 05 Jul 2019 19:47:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX148612/SRX148612.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:47:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX148612/SRX148612.05_summits.bed INFO @ Fri, 05 Jul 2019 19:47:47: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1133 records, 4 fields): 4 millis INFO @ Fri, 05 Jul 2019 19:47:48: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 19:47:48: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:47:50: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX148612/SRX148612.10_peaks.xls INFO @ Fri, 05 Jul 2019 19:47:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX148612/SRX148612.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:47:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX148612/SRX148612.10_summits.bed INFO @ Fri, 05 Jul 2019 19:47:50: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (539 records, 4 fields): 4 millis INFO @ Fri, 05 Jul 2019 19:47:50: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX148612/SRX148612.20_peaks.xls INFO @ Fri, 05 Jul 2019 19:47:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX148612/SRX148612.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:47:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX148612/SRX148612.20_summits.bed INFO @ Fri, 05 Jul 2019 19:47:50: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (142 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling BigWig に変換しました。