Job ID = 2007630 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,920,731 reads read : 10,920,731 reads written : 10,920,731 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529749.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: 00:00:01 Multiseed full-index search: 00:07:52 10920731 reads; of these: 10920731 (100.00%) were unpaired; of these: 321452 (2.94%) aligned 0 times 7971731 (73.00%) aligned exactly 1 time 2627548 (24.06%) aligned >1 times 97.06% overall alignment rate Time searching: 00:07:53 Overall time: 00:07:53 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_sort_core] merging from 8 files... [bam_rmdupse_core] 10561239 / 10599279 = 0.9964 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Fri, 05 Jul 2019 16:13:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548232/ERX2548232.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548232/ERX2548232.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548232/ERX2548232.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548232/ERX2548232.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 BedGraph に変換中... INFO @ Fri, 05 Jul 2019 16:13:55: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:13:55: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:13:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548232/ERX2548232.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548232/ERX2548232.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548232/ERX2548232.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548232/ERX2548232.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 16:13:55: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:13:55: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:13:55: #1 tag size is determined as 63 bps INFO @ Fri, 05 Jul 2019 16:13:55: #1 tag size = 63 INFO @ Fri, 05 Jul 2019 16:13:55: #1 total tags in treatment: 38040 INFO @ Fri, 05 Jul 2019 16:13:55: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:13:55: #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 16:13:55: #1 tags after filtering in treatment: 38040 INFO @ Fri, 05 Jul 2019 16:13:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:13:55: #1 finished! INFO @ Fri, 05 Jul 2019 16:13:55: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:13:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:13:55: #2 number of paired peaks: 338 WARNING @ Fri, 05 Jul 2019 16:13:55: Fewer paired peaks (338) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 338 pairs to build model! INFO @ Fri, 05 Jul 2019 16:13:55: start model_add_line... INFO @ Fri, 05 Jul 2019 16:13:55: start X-correlation... INFO @ Fri, 05 Jul 2019 16:13:55: #1 tag size is determined as 63 bps INFO @ Fri, 05 Jul 2019 16:13:55: #1 tag size = 63 INFO @ Fri, 05 Jul 2019 16:13:55: #1 total tags in treatment: 38040 INFO @ Fri, 05 Jul 2019 16:13:55: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:13:55: #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 16:13:55: #1 tags after filtering in treatment: 38040 INFO @ Fri, 05 Jul 2019 16:13:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:13:55: #1 finished! INFO @ Fri, 05 Jul 2019 16:13:55: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:13:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:13:55: end of X-cor INFO @ Fri, 05 Jul 2019 16:13:55: #2 finished! INFO @ Fri, 05 Jul 2019 16:13:55: #2 predicted fragment length is 85 bps INFO @ Fri, 05 Jul 2019 16:13:55: #2 alternative fragment length(s) may be 15,85,139,158,173,243,296,374,392,446,517,542,558,591 bps INFO @ Fri, 05 Jul 2019 16:13:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548232/ERX2548232.05_model.r INFO @ Fri, 05 Jul 2019 16:13:55: #2 number of paired peaks: 338 WARNING @ Fri, 05 Jul 2019 16:13:55: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:13:55: Fewer paired peaks (338) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 338 pairs to build model! INFO @ Fri, 05 Jul 2019 16:13:55: start model_add_line... WARNING @ Fri, 05 Jul 2019 16:13:55: #2 You may need to consider one of the other alternative d(s): 15,85,139,158,173,243,296,374,392,446,517,542,558,591 WARNING @ Fri, 05 Jul 2019 16:13:55: #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 16:13:55: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:13:55: start X-correlation... INFO @ Fri, 05 Jul 2019 16:13:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:13:55: end of X-cor INFO @ Fri, 05 Jul 2019 16:13:55: #2 finished! INFO @ Fri, 05 Jul 2019 16:13:55: #2 predicted fragment length is 85 bps INFO @ Fri, 05 Jul 2019 16:13:55: #2 alternative fragment length(s) may be 15,85,139,158,173,243,296,374,392,446,517,542,558,591 bps INFO @ Fri, 05 Jul 2019 16:13:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548232/ERX2548232.10_model.r WARNING @ Fri, 05 Jul 2019 16:13:55: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:13:55: #2 You may need to consider one of the other alternative d(s): 15,85,139,158,173,243,296,374,392,446,517,542,558,591 WARNING @ Fri, 05 Jul 2019 16:13:55: #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 16:13:55: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:13:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:13:55: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:13:55: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:13:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548232/ERX2548232.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:13:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548232/ERX2548232.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:13:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548232/ERX2548232.05_summits.bed INFO @ Fri, 05 Jul 2019 16:13:55: Done! INFO @ Fri, 05 Jul 2019 16:13:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548232/ERX2548232.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:13:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548232/ERX2548232.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:13:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548232/ERX2548232.10_summits.bed INFO @ Fri, 05 Jul 2019 16:13:55: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (50 records, 4 fields): 3 millis pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (28 records, 4 fields): 1 millis BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 16:13:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548232/ERX2548232.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548232/ERX2548232.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548232/ERX2548232.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548232/ERX2548232.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 16:13:56: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:13:56: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:13:56: #1 tag size is determined as 63 bps INFO @ Fri, 05 Jul 2019 16:13:56: #1 tag size = 63 INFO @ Fri, 05 Jul 2019 16:13:56: #1 total tags in treatment: 38040 INFO @ Fri, 05 Jul 2019 16:13:56: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:13:56: #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 16:13:56: #1 tags after filtering in treatment: 38040 INFO @ Fri, 05 Jul 2019 16:13:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:13:56: #1 finished! INFO @ Fri, 05 Jul 2019 16:13:56: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:13:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:13:56: #2 number of paired peaks: 338 WARNING @ Fri, 05 Jul 2019 16:13:56: Fewer paired peaks (338) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 338 pairs to build model! INFO @ Fri, 05 Jul 2019 16:13:56: start model_add_line... INFO @ Fri, 05 Jul 2019 16:13:56: start X-correlation... INFO @ Fri, 05 Jul 2019 16:13:56: end of X-cor INFO @ Fri, 05 Jul 2019 16:13:56: #2 finished! INFO @ Fri, 05 Jul 2019 16:13:56: #2 predicted fragment length is 85 bps INFO @ Fri, 05 Jul 2019 16:13:56: #2 alternative fragment length(s) may be 15,85,139,158,173,243,296,374,392,446,517,542,558,591 bps INFO @ Fri, 05 Jul 2019 16:13:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548232/ERX2548232.20_model.r WARNING @ Fri, 05 Jul 2019 16:13:56: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:13:56: #2 You may need to consider one of the other alternative d(s): 15,85,139,158,173,243,296,374,392,446,517,542,558,591 WARNING @ Fri, 05 Jul 2019 16:13:56: #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 16:13:56: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:13:56: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 16:13:56: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:13:56: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548232/ERX2548232.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:13:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548232/ERX2548232.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:13:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548232/ERX2548232.20_summits.bed INFO @ Fri, 05 Jul 2019 16:13:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (8 records, 4 fields): 1 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling