Job ID = 2009753 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,448,887 reads read : 1,448,887 reads written : 1,448,887 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR497930.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: 00:00:20 1448887 reads; of these: 1448887 (100.00%) were unpaired; of these: 75798 (5.23%) aligned 0 times 1126947 (77.78%) aligned exactly 1 time 246142 (16.99%) aligned >1 times 94.77% overall alignment rate Time searching: 00:00:20 Overall time: 00:00:20 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] 737389 / 1373089 = 0.5370 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 19:45:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX148609/SRX148609.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX148609/SRX148609.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX148609/SRX148609.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX148609/SRX148609.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 19:45:04: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:45:04: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:45:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX148609/SRX148609.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX148609/SRX148609.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX148609/SRX148609.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX148609/SRX148609.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 19:45:05: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:45:05: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:45:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX148609/SRX148609.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX148609/SRX148609.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX148609/SRX148609.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX148609/SRX148609.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 19:45:06: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:45:06: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:45:08: #1 tag size is determined as 30 bps INFO @ Fri, 05 Jul 2019 19:45:08: #1 tag size = 30 INFO @ Fri, 05 Jul 2019 19:45:08: #1 total tags in treatment: 635700 INFO @ Fri, 05 Jul 2019 19:45:08: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:45:08: #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 19:45:08: #1 tags after filtering in treatment: 635700 INFO @ Fri, 05 Jul 2019 19:45:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:45:08: #1 finished! INFO @ Fri, 05 Jul 2019 19:45:08: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:45:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:45:08: #2 number of paired peaks: 284 WARNING @ Fri, 05 Jul 2019 19:45:08: Fewer paired peaks (284) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 284 pairs to build model! INFO @ Fri, 05 Jul 2019 19:45:08: start model_add_line... INFO @ Fri, 05 Jul 2019 19:45:08: start X-correlation... INFO @ Fri, 05 Jul 2019 19:45:08: end of X-cor INFO @ Fri, 05 Jul 2019 19:45:08: #2 finished! INFO @ Fri, 05 Jul 2019 19:45:08: #2 predicted fragment length is 262 bps INFO @ Fri, 05 Jul 2019 19:45:08: #2 alternative fragment length(s) may be 4,262 bps INFO @ Fri, 05 Jul 2019 19:45:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX148609/SRX148609.05_model.r INFO @ Fri, 05 Jul 2019 19:45:08: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:45:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:45:09: #1 tag size is determined as 30 bps INFO @ Fri, 05 Jul 2019 19:45:09: #1 tag size = 30 INFO @ Fri, 05 Jul 2019 19:45:09: #1 total tags in treatment: 635700 INFO @ Fri, 05 Jul 2019 19:45:09: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:45:09: #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 19:45:09: #1 tags after filtering in treatment: 635700 INFO @ Fri, 05 Jul 2019 19:45:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:45:09: #1 finished! INFO @ Fri, 05 Jul 2019 19:45:09: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:45:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:45:09: #2 number of paired peaks: 284 WARNING @ Fri, 05 Jul 2019 19:45:09: Fewer paired peaks (284) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 284 pairs to build model! INFO @ Fri, 05 Jul 2019 19:45:09: start model_add_line... INFO @ Fri, 05 Jul 2019 19:45:09: start X-correlation... INFO @ Fri, 05 Jul 2019 19:45:09: end of X-cor INFO @ Fri, 05 Jul 2019 19:45:09: #2 finished! INFO @ Fri, 05 Jul 2019 19:45:09: #2 predicted fragment length is 262 bps INFO @ Fri, 05 Jul 2019 19:45:09: #2 alternative fragment length(s) may be 4,262 bps INFO @ Fri, 05 Jul 2019 19:45:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX148609/SRX148609.10_model.r INFO @ Fri, 05 Jul 2019 19:45:09: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:45:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:45:10: #1 tag size is determined as 30 bps INFO @ Fri, 05 Jul 2019 19:45:10: #1 tag size = 30 INFO @ Fri, 05 Jul 2019 19:45:10: #1 total tags in treatment: 635700 INFO @ Fri, 05 Jul 2019 19:45:10: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:45:10: #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 19:45:10: #1 tags after filtering in treatment: 635700 INFO @ Fri, 05 Jul 2019 19:45:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:45:10: #1 finished! INFO @ Fri, 05 Jul 2019 19:45:10: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:45:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:45:10: #2 number of paired peaks: 284 WARNING @ Fri, 05 Jul 2019 19:45:10: Fewer paired peaks (284) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 284 pairs to build model! INFO @ Fri, 05 Jul 2019 19:45:10: start model_add_line... INFO @ Fri, 05 Jul 2019 19:45:10: start X-correlation... INFO @ Fri, 05 Jul 2019 19:45:10: end of X-cor INFO @ Fri, 05 Jul 2019 19:45:10: #2 finished! INFO @ Fri, 05 Jul 2019 19:45:10: #2 predicted fragment length is 262 bps INFO @ Fri, 05 Jul 2019 19:45:10: #2 alternative fragment length(s) may be 4,262 bps INFO @ Fri, 05 Jul 2019 19:45:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX148609/SRX148609.20_model.r INFO @ Fri, 05 Jul 2019 19:45:10: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:45:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:45:12: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:45:13: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX148609/SRX148609.05_peaks.xls INFO @ Fri, 05 Jul 2019 19:45:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX148609/SRX148609.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:45:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX148609/SRX148609.05_summits.bed INFO @ Fri, 05 Jul 2019 19:45:13: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (280 records, 4 fields): 58 millis INFO @ Fri, 05 Jul 2019 19:45:13: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:45:14: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX148609/SRX148609.10_peaks.xls INFO @ Fri, 05 Jul 2019 19:45:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX148609/SRX148609.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:45:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX148609/SRX148609.10_summits.bed INFO @ Fri, 05 Jul 2019 19:45:14: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (94 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 19:45:14: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 19:45:15: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX148609/SRX148609.20_peaks.xls INFO @ Fri, 05 Jul 2019 19:45:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX148609/SRX148609.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:45:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX148609/SRX148609.20_summits.bed INFO @ Fri, 05 Jul 2019 19:45:15: Done! CompletedMACS2peakCalling pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (22 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。