Job ID = 2011813 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,996,357 reads read : 3,992,714 reads written : 1,996,357 reads 0-length : 1,996,357 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: 00:00:28 1996357 reads; of these: 1996357 (100.00%) were unpaired; of these: 615906 (30.85%) aligned 0 times 1220647 (61.14%) aligned exactly 1 time 159804 (8.00%) aligned >1 times 69.15% overall alignment rate Time searching: 00:00:28 Overall time: 00:00:28 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] 456761 / 1380451 = 0.3309 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 @ Sat, 06 Jul 2019 02:44:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5028243/SRX5028243.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5028243/SRX5028243.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5028243/SRX5028243.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5028243/SRX5028243.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, 06 Jul 2019 02:44:34: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:44:34: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:44:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5028243/SRX5028243.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5028243/SRX5028243.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5028243/SRX5028243.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5028243/SRX5028243.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, 06 Jul 2019 02:44:35: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:44:35: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:44:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5028243/SRX5028243.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5028243/SRX5028243.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5028243/SRX5028243.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5028243/SRX5028243.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, 06 Jul 2019 02:44:36: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:44:36: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:44:44: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 02:44:44: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 02:44:44: #1 total tags in treatment: 923690 INFO @ Sat, 06 Jul 2019 02:44:44: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:44:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 02:44:44: #1 tags after filtering in treatment: 923690 INFO @ Sat, 06 Jul 2019 02:44:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 02:44:44: #1 finished! INFO @ Sat, 06 Jul 2019 02:44:44: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:44:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:44:44: #2 number of paired peaks: 118 WARNING @ Sat, 06 Jul 2019 02:44:44: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Sat, 06 Jul 2019 02:44:44: start model_add_line... INFO @ Sat, 06 Jul 2019 02:44:44: start X-correlation... INFO @ Sat, 06 Jul 2019 02:44:44: end of X-cor INFO @ Sat, 06 Jul 2019 02:44:44: #2 finished! INFO @ Sat, 06 Jul 2019 02:44:44: #2 predicted fragment length is 24 bps INFO @ Sat, 06 Jul 2019 02:44:44: #2 alternative fragment length(s) may be 24,42,49,55,62,89,113,135,158,191,194,205,253,266,318,341,399,435,453,482,522,527,535,569 bps INFO @ Sat, 06 Jul 2019 02:44:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5028243/SRX5028243.05_model.r WARNING @ Sat, 06 Jul 2019 02:44:44: #2 Since the d (24) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 06 Jul 2019 02:44:44: #2 You may need to consider one of the other alternative d(s): 24,42,49,55,62,89,113,135,158,191,194,205,253,266,318,341,399,435,453,482,522,527,535,569 WARNING @ Sat, 06 Jul 2019 02:44:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 06 Jul 2019 02:44:44: #3 Call peaks... INFO @ Sat, 06 Jul 2019 02:44:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 02:44:45: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 02:44:45: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 02:44:45: #1 total tags in treatment: 923690 INFO @ Sat, 06 Jul 2019 02:44:45: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:44:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 02:44:45: #1 tags after filtering in treatment: 923690 INFO @ Sat, 06 Jul 2019 02:44:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 02:44:45: #1 finished! INFO @ Sat, 06 Jul 2019 02:44:45: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:44:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:44:45: #2 number of paired peaks: 118 WARNING @ Sat, 06 Jul 2019 02:44:45: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Sat, 06 Jul 2019 02:44:45: start model_add_line... INFO @ Sat, 06 Jul 2019 02:44:45: start X-correlation... INFO @ Sat, 06 Jul 2019 02:44:46: end of X-cor INFO @ Sat, 06 Jul 2019 02:44:46: #2 finished! INFO @ Sat, 06 Jul 2019 02:44:46: #2 predicted fragment length is 24 bps INFO @ Sat, 06 Jul 2019 02:44:46: #2 alternative fragment length(s) may be 24,42,49,55,62,89,113,135,158,191,194,205,253,266,318,341,399,435,453,482,522,527,535,569 bps INFO @ Sat, 06 Jul 2019 02:44:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5028243/SRX5028243.10_model.r WARNING @ Sat, 06 Jul 2019 02:44:46: #2 Since the d (24) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 06 Jul 2019 02:44:46: #2 You may need to consider one of the other alternative d(s): 24,42,49,55,62,89,113,135,158,191,194,205,253,266,318,341,399,435,453,482,522,527,535,569 WARNING @ Sat, 06 Jul 2019 02:44:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 06 Jul 2019 02:44:46: #3 Call peaks... INFO @ Sat, 06 Jul 2019 02:44:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 02:44:47: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 02:44:47: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 02:44:47: #1 total tags in treatment: 923690 INFO @ Sat, 06 Jul 2019 02:44:47: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:44:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 02:44:47: #1 tags after filtering in treatment: 923690 INFO @ Sat, 06 Jul 2019 02:44:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 02:44:47: #1 finished! INFO @ Sat, 06 Jul 2019 02:44:47: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:44:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:44:47: #2 number of paired peaks: 118 WARNING @ Sat, 06 Jul 2019 02:44:47: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Sat, 06 Jul 2019 02:44:47: start model_add_line... INFO @ Sat, 06 Jul 2019 02:44:47: start X-correlation... INFO @ Sat, 06 Jul 2019 02:44:47: end of X-cor INFO @ Sat, 06 Jul 2019 02:44:47: #2 finished! INFO @ Sat, 06 Jul 2019 02:44:47: #2 predicted fragment length is 24 bps INFO @ Sat, 06 Jul 2019 02:44:47: #2 alternative fragment length(s) may be 24,42,49,55,62,89,113,135,158,191,194,205,253,266,318,341,399,435,453,482,522,527,535,569 bps INFO @ Sat, 06 Jul 2019 02:44:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5028243/SRX5028243.20_model.r WARNING @ Sat, 06 Jul 2019 02:44:47: #2 Since the d (24) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 06 Jul 2019 02:44:47: #2 You may need to consider one of the other alternative d(s): 24,42,49,55,62,89,113,135,158,191,194,205,253,266,318,341,399,435,453,482,522,527,535,569 WARNING @ Sat, 06 Jul 2019 02:44:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 06 Jul 2019 02:44:47: #3 Call peaks... INFO @ Sat, 06 Jul 2019 02:44:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 02:44:47: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 02:44:48: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 02:44:48: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5028243/SRX5028243.05_peaks.xls INFO @ Sat, 06 Jul 2019 02:44:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5028243/SRX5028243.05_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 02:44:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5028243/SRX5028243.05_summits.bed INFO @ Sat, 06 Jul 2019 02:44:48: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (3 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:44:49: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5028243/SRX5028243.10_peaks.xls INFO @ Sat, 06 Jul 2019 02:44:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5028243/SRX5028243.10_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 02:44:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5028243/SRX5028243.10_summits.bed INFO @ Sat, 06 Jul 2019 02:44:49: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:44:49: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 02:44:51: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5028243/SRX5028243.20_peaks.xls INFO @ Sat, 06 Jul 2019 02:44:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5028243/SRX5028243.20_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 02:44:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5028243/SRX5028243.20_summits.bed INFO @ Sat, 06 Jul 2019 02:44:51: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。