Job ID = 2007229 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,995,831 reads read : 1,995,831 reads written : 1,995,831 spots read : 1,919,173 reads read : 1,919,173 reads written : 1,919,173 spots read : 1,962,432 reads read : 1,962,432 reads written : 1,962,432 spots read : 1,890,023 reads read : 1,890,023 reads written : 1,890,023 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529639.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529640.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: 00:02:19 7767459 reads; of these: 7767459 (100.00%) were unpaired; of these: 566287 (7.29%) aligned 0 times 6132278 (78.95%) aligned exactly 1 time 1068894 (13.76%) aligned >1 times 92.71% overall alignment rate Time searching: 00:02:19 Overall time: 00:02:19 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] 7071389 / 7201172 = 0.9820 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 15:57:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548199/ERX2548199.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548199/ERX2548199.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548199/ERX2548199.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548199/ERX2548199.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 15:57:00: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:57:00: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:57:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548199/ERX2548199.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548199/ERX2548199.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548199/ERX2548199.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548199/ERX2548199.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 15:57:01: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:57:01: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:57:01: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:57:01: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:57:01: #1 total tags in treatment: 129783 INFO @ Fri, 05 Jul 2019 15:57:01: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:57:01: #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 15:57:01: #1 tags after filtering in treatment: 129783 INFO @ Fri, 05 Jul 2019 15:57:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:57:01: #1 finished! INFO @ Fri, 05 Jul 2019 15:57:01: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:57:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:57:01: #2 number of paired peaks: 447 WARNING @ Fri, 05 Jul 2019 15:57:01: Fewer paired peaks (447) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 447 pairs to build model! INFO @ Fri, 05 Jul 2019 15:57:01: start model_add_line... INFO @ Fri, 05 Jul 2019 15:57:01: start X-correlation... INFO @ Fri, 05 Jul 2019 15:57:01: end of X-cor INFO @ Fri, 05 Jul 2019 15:57:01: #2 finished! INFO @ Fri, 05 Jul 2019 15:57:01: #2 predicted fragment length is 61 bps INFO @ Fri, 05 Jul 2019 15:57:01: #2 alternative fragment length(s) may be 20,61,83,130,171,213,234,279,318,380,396,437,506 bps INFO @ Fri, 05 Jul 2019 15:57:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548199/ERX2548199.05_model.r WARNING @ Fri, 05 Jul 2019 15:57:01: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:57:01: #2 You may need to consider one of the other alternative d(s): 20,61,83,130,171,213,234,279,318,380,396,437,506 WARNING @ Fri, 05 Jul 2019 15:57:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 15:57:01: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:57:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:57:01: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:57:02: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:57:02: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:57:02: #1 total tags in treatment: 129783 INFO @ Fri, 05 Jul 2019 15:57:02: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:57:02: #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 15:57:02: #1 tags after filtering in treatment: 129783 INFO @ Fri, 05 Jul 2019 15:57:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:57:02: #1 finished! INFO @ Fri, 05 Jul 2019 15:57:02: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:57:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:57:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548199/ERX2548199.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:57:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548199/ERX2548199.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:57:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548199/ERX2548199.05_summits.bed INFO @ Fri, 05 Jul 2019 15:57:02: Done! INFO @ Fri, 05 Jul 2019 15:57:02: #2 number of paired peaks: 447 WARNING @ Fri, 05 Jul 2019 15:57:02: Fewer paired peaks (447) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 447 pairs to build model! INFO @ Fri, 05 Jul 2019 15:57:02: start model_add_line... INFO @ Fri, 05 Jul 2019 15:57:02: start X-correlation... INFO @ Fri, 05 Jul 2019 15:57:02: end of X-cor INFO @ Fri, 05 Jul 2019 15:57:02: #2 finished! INFO @ Fri, 05 Jul 2019 15:57:02: #2 predicted fragment length is 61 bps INFO @ Fri, 05 Jul 2019 15:57:02: #2 alternative fragment length(s) may be 20,61,83,130,171,213,234,279,318,380,396,437,506 bps INFO @ Fri, 05 Jul 2019 15:57:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548199/ERX2548199.10_model.r WARNING @ Fri, 05 Jul 2019 15:57:02: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:57:02: #2 You may need to consider one of the other alternative d(s): 20,61,83,130,171,213,234,279,318,380,396,437,506 WARNING @ Fri, 05 Jul 2019 15:57:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 15:57:02: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:57:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:57:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548199/ERX2548199.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548199/ERX2548199.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548199/ERX2548199.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548199/ERX2548199.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 15:57:02: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:57:02: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:57:02: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:57:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548199/ERX2548199.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:57:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548199/ERX2548199.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:57:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548199/ERX2548199.10_summits.bed INFO @ Fri, 05 Jul 2019 15:57:02: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (55 records, 4 fields): 3 millis pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (14 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 15:57:03: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:57:03: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:57:03: #1 total tags in treatment: 129783 INFO @ Fri, 05 Jul 2019 15:57:03: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:57:03: #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 15:57:03: #1 tags after filtering in treatment: 129783 INFO @ Fri, 05 Jul 2019 15:57:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:57:03: #1 finished! INFO @ Fri, 05 Jul 2019 15:57:03: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:57:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:57:03: #2 number of paired peaks: 447 WARNING @ Fri, 05 Jul 2019 15:57:03: Fewer paired peaks (447) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 447 pairs to build model! INFO @ Fri, 05 Jul 2019 15:57:03: start model_add_line... INFO @ Fri, 05 Jul 2019 15:57:03: start X-correlation... INFO @ Fri, 05 Jul 2019 15:57:03: end of X-cor INFO @ Fri, 05 Jul 2019 15:57:03: #2 finished! INFO @ Fri, 05 Jul 2019 15:57:03: #2 predicted fragment length is 61 bps INFO @ Fri, 05 Jul 2019 15:57:03: #2 alternative fragment length(s) may be 20,61,83,130,171,213,234,279,318,380,396,437,506 bps INFO @ Fri, 05 Jul 2019 15:57:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548199/ERX2548199.20_model.r WARNING @ Fri, 05 Jul 2019 15:57:03: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:57:03: #2 You may need to consider one of the other alternative d(s): 20,61,83,130,171,213,234,279,318,380,396,437,506 WARNING @ Fri, 05 Jul 2019 15:57:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 15:57:03: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:57:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:57:04: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:57:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548199/ERX2548199.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:57:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548199/ERX2548199.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:57:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548199/ERX2548199.20_summits.bed INFO @ Fri, 05 Jul 2019 15:57:04: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。