Job ID = 2008384 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,420,699 reads read : 5,420,699 reads written : 5,420,699 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR637556.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: 00:00:52 5420699 reads; of these: 5420699 (100.00%) were unpaired; of these: 3999517 (73.78%) aligned 0 times 1067980 (19.70%) aligned exactly 1 time 353202 (6.52%) aligned >1 times 26.22% overall alignment rate Time searching: 00:00:52 Overall time: 00:00:52 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] 484340 / 1421182 = 0.3408 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 18:55:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX593998/ERX593998.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX593998/ERX593998.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX593998/ERX593998.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX593998/ERX593998.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 18:55:01: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:55:01: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:55:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX593998/ERX593998.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX593998/ERX593998.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX593998/ERX593998.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX593998/ERX593998.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 18:55:02: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:55:02: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:55:09: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 18:55:09: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 18:55:09: #1 total tags in treatment: 936842 INFO @ Fri, 05 Jul 2019 18:55:09: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:55:09: #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 18:55:09: #1 tags after filtering in treatment: 936842 INFO @ Fri, 05 Jul 2019 18:55:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 18:55:09: #1 finished! INFO @ Fri, 05 Jul 2019 18:55:09: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:55:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:55:09: #2 number of paired peaks: 386 WARNING @ Fri, 05 Jul 2019 18:55:09: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Fri, 05 Jul 2019 18:55:09: start model_add_line... INFO @ Fri, 05 Jul 2019 18:55:09: start X-correlation... INFO @ Fri, 05 Jul 2019 18:55:09: end of X-cor INFO @ Fri, 05 Jul 2019 18:55:09: #2 finished! INFO @ Fri, 05 Jul 2019 18:55:09: #2 predicted fragment length is 174 bps INFO @ Fri, 05 Jul 2019 18:55:09: #2 alternative fragment length(s) may be 174 bps INFO @ Fri, 05 Jul 2019 18:55:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX593998/ERX593998.05_model.r INFO @ Fri, 05 Jul 2019 18:55:09: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:55:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:55:10: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 18:55:10: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 18:55:10: #1 total tags in treatment: 936842 INFO @ Fri, 05 Jul 2019 18:55:10: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:55:10: #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 18:55:10: #1 tags after filtering in treatment: 936842 INFO @ Fri, 05 Jul 2019 18:55:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 18:55:10: #1 finished! INFO @ Fri, 05 Jul 2019 18:55:10: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:55:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:55:10: #2 number of paired peaks: 386 WARNING @ Fri, 05 Jul 2019 18:55:10: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Fri, 05 Jul 2019 18:55:10: start model_add_line... INFO @ Fri, 05 Jul 2019 18:55:10: start X-correlation... INFO @ Fri, 05 Jul 2019 18:55:10: end of X-cor INFO @ Fri, 05 Jul 2019 18:55:10: #2 finished! INFO @ Fri, 05 Jul 2019 18:55:10: #2 predicted fragment length is 174 bps INFO @ Fri, 05 Jul 2019 18:55:10: #2 alternative fragment length(s) may be 174 bps INFO @ Fri, 05 Jul 2019 18:55:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX593998/ERX593998.10_model.r INFO @ Fri, 05 Jul 2019 18:55:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX593998/ERX593998.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX593998/ERX593998.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX593998/ERX593998.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX593998/ERX593998.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 18:55:10: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:55:10: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:55:12: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:55:14: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX593998/ERX593998.05_peaks.xls INFO @ Fri, 05 Jul 2019 18:55:19: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 18:55:19: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 18:55:19: #1 total tags in treatment: 936842 INFO @ Fri, 05 Jul 2019 18:55:19: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:55:19: #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 18:55:19: #1 tags after filtering in treatment: 936842 INFO @ Fri, 05 Jul 2019 18:55:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 18:55:19: #1 finished! INFO @ Fri, 05 Jul 2019 18:55:19: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:55:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:55:19: #2 number of paired peaks: 386 WARNING @ Fri, 05 Jul 2019 18:55:19: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Fri, 05 Jul 2019 18:55:19: start model_add_line... INFO @ Fri, 05 Jul 2019 18:55:19: start X-correlation... INFO @ Fri, 05 Jul 2019 18:55:19: end of X-cor INFO @ Fri, 05 Jul 2019 18:55:19: #2 finished! INFO @ Fri, 05 Jul 2019 18:55:19: #2 predicted fragment length is 174 bps INFO @ Fri, 05 Jul 2019 18:55:19: #2 alternative fragment length(s) may be 174 bps INFO @ Fri, 05 Jul 2019 18:55:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX593998/ERX593998.20_model.r INFO @ Fri, 05 Jul 2019 18:55:25: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:55:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:55:25: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:55:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:55:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX593998/ERX593998.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:55:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX593998/ERX593998.05_summits.bed INFO @ Fri, 05 Jul 2019 18:55:25: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (2065 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 18:55:28: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:55:28: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:55:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX593998/ERX593998.20_peaks.xls INFO @ Fri, 05 Jul 2019 18:55:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX593998/ERX593998.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:55:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX593998/ERX593998.20_summits.bed INFO @ Fri, 05 Jul 2019 18:55:30: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (849 records, 4 fields): 5 millis INFO @ Fri, 05 Jul 2019 18:55:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX593998/ERX593998.10_peaks.xls INFO @ Fri, 05 Jul 2019 18:55:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX593998/ERX593998.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:55:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX593998/ERX593998.10_summits.bed INFO @ Fri, 05 Jul 2019 18:55:30: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (1419 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。 CompletedMACS2peakCalling