Job ID = 2009012 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,807,650 reads read : 2,807,650 reads written : 2,807,650 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR637566.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: 00:00:30 2807650 reads; of these: 2807650 (100.00%) were unpaired; of these: 1844202 (65.68%) aligned 0 times 724048 (25.79%) aligned exactly 1 time 239400 (8.53%) aligned >1 times 34.32% overall alignment rate Time searching: 00:00:30 Overall time: 00:00:30 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] 362742 / 963448 = 0.3765 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 19:08:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594029/ERX594029.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594029/ERX594029.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594029/ERX594029.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594029/ERX594029.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 19:08:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594029/ERX594029.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594029/ERX594029.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594029/ERX594029.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594029/ERX594029.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 19:08:06: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:08:06: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:08:06: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:08:06: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:08:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594029/ERX594029.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594029/ERX594029.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594029/ERX594029.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594029/ERX594029.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 19:08:06: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:08:06: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:08:12: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 19:08:12: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 19:08:12: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 19:08:12: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 19:08:12: #1 total tags in treatment: 600706 INFO @ Fri, 05 Jul 2019 19:08:12: #1 total tags in treatment: 600706 INFO @ Fri, 05 Jul 2019 19:08:12: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:08:12: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:08:12: #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 19:08:12: #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 19:08:12: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 19:08:12: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 19:08:12: #1 total tags in treatment: 600706 INFO @ Fri, 05 Jul 2019 19:08:12: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:08:12: #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 19:08:12: #1 tags after filtering in treatment: 600706 INFO @ Fri, 05 Jul 2019 19:08:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:08:12: #1 finished! INFO @ Fri, 05 Jul 2019 19:08:12: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:08:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:08:12: #1 tags after filtering in treatment: 600706 INFO @ Fri, 05 Jul 2019 19:08:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:08:12: #1 finished! INFO @ Fri, 05 Jul 2019 19:08:12: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:08:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:08:12: #1 tags after filtering in treatment: 600706 INFO @ Fri, 05 Jul 2019 19:08:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:08:12: #1 finished! INFO @ Fri, 05 Jul 2019 19:08:12: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:08:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:08:12: #2 number of paired peaks: 235 WARNING @ Fri, 05 Jul 2019 19:08:12: Fewer paired peaks (235) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 235 pairs to build model! INFO @ Fri, 05 Jul 2019 19:08:12: start model_add_line... INFO @ Fri, 05 Jul 2019 19:08:12: #2 number of paired peaks: 235 WARNING @ Fri, 05 Jul 2019 19:08:12: Fewer paired peaks (235) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 235 pairs to build model! INFO @ Fri, 05 Jul 2019 19:08:12: start model_add_line... INFO @ Fri, 05 Jul 2019 19:08:12: #2 number of paired peaks: 235 WARNING @ Fri, 05 Jul 2019 19:08:12: Fewer paired peaks (235) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 235 pairs to build model! INFO @ Fri, 05 Jul 2019 19:08:12: start model_add_line... INFO @ Fri, 05 Jul 2019 19:08:12: start X-correlation... INFO @ Fri, 05 Jul 2019 19:08:12: start X-correlation... INFO @ Fri, 05 Jul 2019 19:08:12: start X-correlation... INFO @ Fri, 05 Jul 2019 19:08:12: end of X-cor INFO @ Fri, 05 Jul 2019 19:08:12: #2 finished! INFO @ Fri, 05 Jul 2019 19:08:12: #2 predicted fragment length is 144 bps INFO @ Fri, 05 Jul 2019 19:08:12: end of X-cor INFO @ Fri, 05 Jul 2019 19:08:12: #2 alternative fragment length(s) may be 144 bps INFO @ Fri, 05 Jul 2019 19:08:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594029/ERX594029.20_model.r INFO @ Fri, 05 Jul 2019 19:08:12: #2 finished! INFO @ Fri, 05 Jul 2019 19:08:12: #2 predicted fragment length is 144 bps INFO @ Fri, 05 Jul 2019 19:08:12: end of X-cor INFO @ Fri, 05 Jul 2019 19:08:12: #2 alternative fragment length(s) may be 144 bps INFO @ Fri, 05 Jul 2019 19:08:12: #2 finished! INFO @ Fri, 05 Jul 2019 19:08:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594029/ERX594029.05_model.r INFO @ Fri, 05 Jul 2019 19:08:12: #2 predicted fragment length is 144 bps INFO @ Fri, 05 Jul 2019 19:08:12: #2 alternative fragment length(s) may be 144 bps INFO @ Fri, 05 Jul 2019 19:08:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594029/ERX594029.10_model.r BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 19:08:42: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:08:42: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:08:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:08:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:08:44: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:08:44: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 19:08:45: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:08:45: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:08:46: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594029/ERX594029.20_peaks.xls INFO @ Fri, 05 Jul 2019 19:08:46: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594029/ERX594029.05_peaks.xls INFO @ Fri, 05 Jul 2019 19:08:46: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:08:47: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594029/ERX594029.10_peaks.xls INFO @ Fri, 05 Jul 2019 19:08:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594029/ERX594029.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:08:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594029/ERX594029.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:08:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594029/ERX594029.20_summits.bed INFO @ Fri, 05 Jul 2019 19:08:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594029/ERX594029.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:08:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594029/ERX594029.10_summits.bed INFO @ Fri, 05 Jul 2019 19:08:56: Done! INFO @ Fri, 05 Jul 2019 19:08:56: Done! INFO @ Fri, 05 Jul 2019 19:08:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594029/ERX594029.05_summits.bed INFO @ Fri, 05 Jul 2019 19:08:56: Done! pass1 - making usageList (16 chroms)pass1 - making usageList (16 chroms): 1 millis : 2 millis pass2 - checking and writing primary data (507 records, 4 fields): 9 millis pass2 - checking and writing primary data (810 records, 4 fields): 10 millis pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (267 records, 4 fields): 3 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling