Job ID = 2003800 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 917,638 reads read : 917,638 reads written : 917,638 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: 00:00:06 917638 reads; of these: 917638 (100.00%) were unpaired; of these: 693529 (75.58%) aligned 0 times 193405 (21.08%) aligned exactly 1 time 30704 (3.35%) aligned >1 times 24.42% overall alignment rate Time searching: 00:00:06 Overall time: 00:00:06 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] 14203 / 224109 = 0.0634 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 14:14:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX008713/ERX008713.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX008713/ERX008713.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX008713/ERX008713.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX008713/ERX008713.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 14:14:51: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:14:51: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:14:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX008713/ERX008713.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX008713/ERX008713.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX008713/ERX008713.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX008713/ERX008713.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 14:14:52: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:14:52: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:14:52: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 14:14:52: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 14:14:52: #1 total tags in treatment: 209906 INFO @ Fri, 05 Jul 2019 14:14:52: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:14:52: #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 14:14:52: #1 tags after filtering in treatment: 209906 INFO @ Fri, 05 Jul 2019 14:14:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:14:52: #1 finished! INFO @ Fri, 05 Jul 2019 14:14:52: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:14:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:14:52: #2 number of paired peaks: 260 WARNING @ Fri, 05 Jul 2019 14:14:52: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Fri, 05 Jul 2019 14:14:52: start model_add_line... INFO @ Fri, 05 Jul 2019 14:14:52: start X-correlation... INFO @ Fri, 05 Jul 2019 14:14:52: end of X-cor INFO @ Fri, 05 Jul 2019 14:14:52: #2 finished! INFO @ Fri, 05 Jul 2019 14:14:52: #2 predicted fragment length is 142 bps INFO @ Fri, 05 Jul 2019 14:14:52: #2 alternative fragment length(s) may be 142,584 bps INFO @ Fri, 05 Jul 2019 14:14:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX008713/ERX008713.05_model.r INFO @ Fri, 05 Jul 2019 14:14:52: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:14:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:14:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX008713/ERX008713.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX008713/ERX008713.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX008713/ERX008713.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX008713/ERX008713.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 14:14:53: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:14:53: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:14:53: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:14:53: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 14:14:53: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 14:14:53: #1 total tags in treatment: 209906 INFO @ Fri, 05 Jul 2019 14:14:53: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:14:53: #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 14:14:53: #1 tags after filtering in treatment: 209906 INFO @ Fri, 05 Jul 2019 14:14:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:14:53: #1 finished! INFO @ Fri, 05 Jul 2019 14:14:53: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:14:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:14:53: #2 number of paired peaks: 260 WARNING @ Fri, 05 Jul 2019 14:14:53: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Fri, 05 Jul 2019 14:14:53: start model_add_line... INFO @ Fri, 05 Jul 2019 14:14:53: start X-correlation... INFO @ Fri, 05 Jul 2019 14:14:53: end of X-cor INFO @ Fri, 05 Jul 2019 14:14:53: #2 finished! INFO @ Fri, 05 Jul 2019 14:14:53: #2 predicted fragment length is 142 bps INFO @ Fri, 05 Jul 2019 14:14:53: #2 alternative fragment length(s) may be 142,584 bps INFO @ Fri, 05 Jul 2019 14:14:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX008713/ERX008713.10_model.r INFO @ Fri, 05 Jul 2019 14:14:53: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:14:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:14:53: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX008713/ERX008713.05_peaks.xls INFO @ Fri, 05 Jul 2019 14:14:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX008713/ERX008713.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:14:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX008713/ERX008713.05_summits.bed INFO @ Fri, 05 Jul 2019 14:14:53: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (311 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 14:14:54: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:14:54: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX008713/ERX008713.10_peaks.xls INFO @ Fri, 05 Jul 2019 14:14:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX008713/ERX008713.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:14:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX008713/ERX008713.10_summits.bed INFO @ Fri, 05 Jul 2019 14:14:54: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (121 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 14:14:55: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 14:14:55: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 14:14:55: #1 total tags in treatment: 209906 INFO @ Fri, 05 Jul 2019 14:14:55: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:14:55: #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 14:14:55: #1 tags after filtering in treatment: 209906 INFO @ Fri, 05 Jul 2019 14:14:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:14:55: #1 finished! INFO @ Fri, 05 Jul 2019 14:14:55: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:14:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:14:55: #2 number of paired peaks: 260 WARNING @ Fri, 05 Jul 2019 14:14:55: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Fri, 05 Jul 2019 14:14:55: start model_add_line... INFO @ Fri, 05 Jul 2019 14:14:55: start X-correlation... INFO @ Fri, 05 Jul 2019 14:14:55: end of X-cor INFO @ Fri, 05 Jul 2019 14:14:55: #2 finished! INFO @ Fri, 05 Jul 2019 14:14:55: #2 predicted fragment length is 142 bps INFO @ Fri, 05 Jul 2019 14:14:55: #2 alternative fragment length(s) may be 142,584 bps INFO @ Fri, 05 Jul 2019 14:14:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX008713/ERX008713.20_model.r INFO @ Fri, 05 Jul 2019 14:14:55: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:14:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:14:56: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:14:56: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX008713/ERX008713.20_peaks.xls CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 14:14:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX008713/ERX008713.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:14:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX008713/ERX008713.20_summits.bed INFO @ Fri, 05 Jul 2019 14:14:57: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (42 records, 4 fields): 3 millis BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 CompletedMACS2peakCalling CompletedMACS2peakCalling