Job ID = 2640959 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 710,040 reads read : 710,040 reads written : 710,040 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1197812.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: 00:00:08 710040 reads; of these: 710040 (100.00%) were unpaired; of these: 391629 (55.16%) aligned 0 times 263553 (37.12%) aligned exactly 1 time 54858 (7.73%) aligned >1 times 44.84% overall alignment rate Time searching: 00:00:08 Overall time: 00:00:08 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] 153700 / 318411 = 0.4827 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 20:05:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX472142/SRX472142.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX472142/SRX472142.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX472142/SRX472142.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX472142/SRX472142.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 @ Sat, 24 Aug 2019 20:05:11: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:05:11: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:05:12: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 20:05:12: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 20:05:12: #1 total tags in treatment: 164711 INFO @ Sat, 24 Aug 2019 20:05:12: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:05:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 20:05:12: #1 tags after filtering in treatment: 164711 INFO @ Sat, 24 Aug 2019 20:05:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:05:12: #1 finished! INFO @ Sat, 24 Aug 2019 20:05:12: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:05:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:05:12: #2 number of paired peaks: 120 WARNING @ Sat, 24 Aug 2019 20:05:12: Fewer paired peaks (120) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 120 pairs to build model! INFO @ Sat, 24 Aug 2019 20:05:12: start model_add_line... INFO @ Sat, 24 Aug 2019 20:05:12: start X-correlation... INFO @ Sat, 24 Aug 2019 20:05:12: end of X-cor INFO @ Sat, 24 Aug 2019 20:05:12: #2 finished! INFO @ Sat, 24 Aug 2019 20:05:12: #2 predicted fragment length is 125 bps INFO @ Sat, 24 Aug 2019 20:05:12: #2 alternative fragment length(s) may be 125 bps INFO @ Sat, 24 Aug 2019 20:05:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX472142/SRX472142.05_model.r INFO @ Sat, 24 Aug 2019 20:05:12: #3 Call peaks... INFO @ Sat, 24 Aug 2019 20:05:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 20:05:13: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 20:05:13: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX472142/SRX472142.05_peaks.xls INFO @ Sat, 24 Aug 2019 20:05:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX472142/SRX472142.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 20:05:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX472142/SRX472142.05_summits.bed INFO @ Sat, 24 Aug 2019 20:05:13: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (191 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 20:05:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX472142/SRX472142.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX472142/SRX472142.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX472142/SRX472142.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX472142/SRX472142.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 @ Sat, 24 Aug 2019 20:05:41: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:05:41: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:05:42: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 20:05:42: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 20:05:42: #1 total tags in treatment: 164711 INFO @ Sat, 24 Aug 2019 20:05:42: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:05:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 20:05:42: #1 tags after filtering in treatment: 164711 INFO @ Sat, 24 Aug 2019 20:05:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:05:42: #1 finished! INFO @ Sat, 24 Aug 2019 20:05:42: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:05:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:05:42: #2 number of paired peaks: 120 WARNING @ Sat, 24 Aug 2019 20:05:42: Fewer paired peaks (120) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 120 pairs to build model! INFO @ Sat, 24 Aug 2019 20:05:42: start model_add_line... INFO @ Sat, 24 Aug 2019 20:05:42: start X-correlation... INFO @ Sat, 24 Aug 2019 20:05:42: end of X-cor INFO @ Sat, 24 Aug 2019 20:05:42: #2 finished! INFO @ Sat, 24 Aug 2019 20:05:42: #2 predicted fragment length is 125 bps INFO @ Sat, 24 Aug 2019 20:05:42: #2 alternative fragment length(s) may be 125 bps INFO @ Sat, 24 Aug 2019 20:05:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX472142/SRX472142.10_model.r INFO @ Sat, 24 Aug 2019 20:05:42: #3 Call peaks... INFO @ Sat, 24 Aug 2019 20:05:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 20:05:43: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 20:05:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX472142/SRX472142.10_peaks.xls INFO @ Sat, 24 Aug 2019 20:05:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX472142/SRX472142.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 20:05:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX472142/SRX472142.10_summits.bed INFO @ Sat, 24 Aug 2019 20:05:43: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (54 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Sat, 24 Aug 2019 20:06:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX472142/SRX472142.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX472142/SRX472142.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX472142/SRX472142.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX472142/SRX472142.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 @ Sat, 24 Aug 2019 20:06:11: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:06:11: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 20:06:12: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 20:06:12: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 20:06:12: #1 total tags in treatment: 164711 INFO @ Sat, 24 Aug 2019 20:06:12: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:06:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 20:06:12: #1 tags after filtering in treatment: 164711 INFO @ Sat, 24 Aug 2019 20:06:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:06:12: #1 finished! INFO @ Sat, 24 Aug 2019 20:06:12: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:06:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:06:13: #2 number of paired peaks: 120 WARNING @ Sat, 24 Aug 2019 20:06:13: Fewer paired peaks (120) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 120 pairs to build model! INFO @ Sat, 24 Aug 2019 20:06:13: start model_add_line... INFO @ Sat, 24 Aug 2019 20:06:13: start X-correlation... INFO @ Sat, 24 Aug 2019 20:06:13: end of X-cor INFO @ Sat, 24 Aug 2019 20:06:13: #2 finished! INFO @ Sat, 24 Aug 2019 20:06:13: #2 predicted fragment length is 125 bps INFO @ Sat, 24 Aug 2019 20:06:13: #2 alternative fragment length(s) may be 125 bps INFO @ Sat, 24 Aug 2019 20:06:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX472142/SRX472142.20_model.r INFO @ Sat, 24 Aug 2019 20:06:13: #3 Call peaks... INFO @ Sat, 24 Aug 2019 20:06:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 20:06:13: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 20:06:13: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX472142/SRX472142.20_peaks.xls INFO @ Sat, 24 Aug 2019 20:06:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX472142/SRX472142.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 20:06:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX472142/SRX472142.20_summits.bed INFO @ Sat, 24 Aug 2019 20:06:13: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (5 records, 4 fields): 2 millis CompletedMACS2peakCalling