Job ID = 2006283 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,127,166 reads read : 2,127,166 reads written : 2,127,166 spots read : 2,030,666 reads read : 2,030,666 reads written : 2,030,666 spots read : 2,047,413 reads read : 2,047,413 reads written : 2,047,413 spots read : 2,033,390 reads read : 2,033,390 reads written : 2,033,390 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529422.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529423.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529425.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: 00:03:56 8238635 reads; of these: 8238635 (100.00%) were unpaired; of these: 662084 (8.04%) aligned 0 times 5886041 (71.44%) aligned exactly 1 time 1690510 (20.52%) aligned >1 times 91.96% overall alignment rate Time searching: 00:03:56 Overall time: 00:03:56 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] 7170804 / 7576551 = 0.9464 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 15:24:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548133/ERX2548133.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548133/ERX2548133.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548133/ERX2548133.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548133/ERX2548133.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 15:24:15: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:24:15: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:24:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548133/ERX2548133.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548133/ERX2548133.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548133/ERX2548133.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548133/ERX2548133.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 15:24:17: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:24:17: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:24:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548133/ERX2548133.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548133/ERX2548133.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548133/ERX2548133.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548133/ERX2548133.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 15:24:18: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:24:18: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:24:19: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:24:19: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:24:19: #1 total tags in treatment: 405747 INFO @ Fri, 05 Jul 2019 15:24:19: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:24:19: #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 15:24:19: #1 tags after filtering in treatment: 405747 INFO @ Fri, 05 Jul 2019 15:24:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:24:19: #1 finished! INFO @ Fri, 05 Jul 2019 15:24:19: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:24:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:24:19: #2 number of paired peaks: 446 WARNING @ Fri, 05 Jul 2019 15:24:19: Fewer paired peaks (446) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 446 pairs to build model! INFO @ Fri, 05 Jul 2019 15:24:19: start model_add_line... INFO @ Fri, 05 Jul 2019 15:24:19: start X-correlation... INFO @ Fri, 05 Jul 2019 15:24:19: end of X-cor INFO @ Fri, 05 Jul 2019 15:24:19: #2 finished! INFO @ Fri, 05 Jul 2019 15:24:19: #2 predicted fragment length is 91 bps INFO @ Fri, 05 Jul 2019 15:24:19: #2 alternative fragment length(s) may be 91 bps INFO @ Fri, 05 Jul 2019 15:24:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548133/ERX2548133.05_model.r WARNING @ Fri, 05 Jul 2019 15:24:19: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:24:19: #2 You may need to consider one of the other alternative d(s): 91 WARNING @ Fri, 05 Jul 2019 15:24:19: #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 15:24:19: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:24:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:24:20: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:24:20: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:24:20: #1 total tags in treatment: 405747 INFO @ Fri, 05 Jul 2019 15:24:20: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:24:20: #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 15:24:20: #1 tags after filtering in treatment: 405747 INFO @ Fri, 05 Jul 2019 15:24:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:24:20: #1 finished! INFO @ Fri, 05 Jul 2019 15:24:20: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:24:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:24:20: #2 number of paired peaks: 446 WARNING @ Fri, 05 Jul 2019 15:24:20: Fewer paired peaks (446) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 446 pairs to build model! INFO @ Fri, 05 Jul 2019 15:24:20: start model_add_line... INFO @ Fri, 05 Jul 2019 15:24:20: start X-correlation... INFO @ Fri, 05 Jul 2019 15:24:20: end of X-cor INFO @ Fri, 05 Jul 2019 15:24:20: #2 finished! INFO @ Fri, 05 Jul 2019 15:24:20: #2 predicted fragment length is 91 bps INFO @ Fri, 05 Jul 2019 15:24:20: #2 alternative fragment length(s) may be 91 bps INFO @ Fri, 05 Jul 2019 15:24:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548133/ERX2548133.10_model.r WARNING @ Fri, 05 Jul 2019 15:24:20: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:24:20: #2 You may need to consider one of the other alternative d(s): 91 WARNING @ Fri, 05 Jul 2019 15:24:20: #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 15:24:20: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:24:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:24:21: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:24:21: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548133/ERX2548133.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:24:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548133/ERX2548133.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:24:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548133/ERX2548133.05_summits.bed INFO @ Fri, 05 Jul 2019 15:24:21: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (227 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 15:24:22: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:24:22: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:24:22: #1 total tags in treatment: 405747 INFO @ Fri, 05 Jul 2019 15:24:22: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:24:22: #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 15:24:22: #1 tags after filtering in treatment: 405747 INFO @ Fri, 05 Jul 2019 15:24:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:24:22: #1 finished! INFO @ Fri, 05 Jul 2019 15:24:22: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:24:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:24:22: #2 number of paired peaks: 446 WARNING @ Fri, 05 Jul 2019 15:24:22: Fewer paired peaks (446) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 446 pairs to build model! INFO @ Fri, 05 Jul 2019 15:24:22: start model_add_line... INFO @ Fri, 05 Jul 2019 15:24:22: start X-correlation... INFO @ Fri, 05 Jul 2019 15:24:22: end of X-cor INFO @ Fri, 05 Jul 2019 15:24:22: #2 finished! INFO @ Fri, 05 Jul 2019 15:24:22: #2 predicted fragment length is 91 bps INFO @ Fri, 05 Jul 2019 15:24:22: #2 alternative fragment length(s) may be 91 bps INFO @ Fri, 05 Jul 2019 15:24:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548133/ERX2548133.20_model.r WARNING @ Fri, 05 Jul 2019 15:24:22: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:24:22: #2 You may need to consider one of the other alternative d(s): 91 WARNING @ Fri, 05 Jul 2019 15:24:22: #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 15:24:22: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:24:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:24:22: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:24:23: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548133/ERX2548133.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:24:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548133/ERX2548133.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:24:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548133/ERX2548133.10_summits.bed INFO @ Fri, 05 Jul 2019 15:24:23: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (177 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 15:24:24: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 15:24:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548133/ERX2548133.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:24:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548133/ERX2548133.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:24:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548133/ERX2548133.20_summits.bed INFO @ Fri, 05 Jul 2019 15:24:24: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (164 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 CompletedMACS2peakCalling CompletedMACS2peakCalling