Job ID = 2006623 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,412,123 reads read : 1,412,123 reads written : 1,412,123 spots read : 1,400,944 reads read : 1,400,944 reads written : 1,400,944 spots read : 1,378,964 reads read : 1,378,964 reads written : 1,378,964 spots read : 1,340,295 reads read : 1,340,295 reads written : 1,340,295 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529534.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529535.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529537.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: 00:04:17 5532326 reads; of these: 5532326 (100.00%) were unpaired; of these: 184852 (3.34%) aligned 0 times 4502413 (81.38%) aligned exactly 1 time 845061 (15.27%) aligned >1 times 96.66% overall alignment rate Time searching: 00:04:17 Overall time: 00:04:17 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] 5212923 / 5347474 = 0.9748 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 15:50:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548167/ERX2548167.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548167/ERX2548167.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548167/ERX2548167.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548167/ERX2548167.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 15:50:36: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:50:36: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:50:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548167/ERX2548167.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548167/ERX2548167.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548167/ERX2548167.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548167/ERX2548167.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 15:50:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:50:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:50:37: #1 tag size is determined as 148 bps INFO @ Fri, 05 Jul 2019 15:50:37: #1 tag size = 148 INFO @ Fri, 05 Jul 2019 15:50:37: #1 total tags in treatment: 134551 INFO @ Fri, 05 Jul 2019 15:50:37: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:50:37: #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 15:50:37: #1 tags after filtering in treatment: 134551 INFO @ Fri, 05 Jul 2019 15:50:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:50:37: #1 finished! INFO @ Fri, 05 Jul 2019 15:50:37: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:50:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:50:37: #2 number of paired peaks: 242 WARNING @ Fri, 05 Jul 2019 15:50:37: Fewer paired peaks (242) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 242 pairs to build model! INFO @ Fri, 05 Jul 2019 15:50:37: start model_add_line... INFO @ Fri, 05 Jul 2019 15:50:37: start X-correlation... INFO @ Fri, 05 Jul 2019 15:50:37: end of X-cor INFO @ Fri, 05 Jul 2019 15:50:37: #2 finished! INFO @ Fri, 05 Jul 2019 15:50:37: #2 predicted fragment length is 180 bps INFO @ Fri, 05 Jul 2019 15:50:37: #2 alternative fragment length(s) may be 62,119,151,180,201,238,255,290,303,373,387,439,457,523,598 bps INFO @ Fri, 05 Jul 2019 15:50:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548167/ERX2548167.05_model.r WARNING @ Fri, 05 Jul 2019 15:50:37: #2 Since the d (180) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:50:37: #2 You may need to consider one of the other alternative d(s): 62,119,151,180,201,238,255,290,303,373,387,439,457,523,598 WARNING @ Fri, 05 Jul 2019 15:50:37: #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 15:50:37: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:50:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:50:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548167/ERX2548167.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548167/ERX2548167.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548167/ERX2548167.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548167/ERX2548167.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 15:50:38: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:50:38: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:50:38: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:50:38: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548167/ERX2548167.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:50:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548167/ERX2548167.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:50:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548167/ERX2548167.05_summits.bed INFO @ Fri, 05 Jul 2019 15:50:38: Done! INFO @ Fri, 05 Jul 2019 15:50:38: #1 tag size is determined as 148 bps INFO @ Fri, 05 Jul 2019 15:50:38: #1 tag size = 148 INFO @ Fri, 05 Jul 2019 15:50:38: #1 total tags in treatment: 134551 INFO @ Fri, 05 Jul 2019 15:50:38: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:50:38: #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 15:50:38: #1 tags after filtering in treatment: 134551 INFO @ Fri, 05 Jul 2019 15:50:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:50:38: #1 finished! INFO @ Fri, 05 Jul 2019 15:50:38: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:50:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:50:38: #2 number of paired peaks: 242 WARNING @ Fri, 05 Jul 2019 15:50:38: Fewer paired peaks (242) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 242 pairs to build model! INFO @ Fri, 05 Jul 2019 15:50:38: start model_add_line... INFO @ Fri, 05 Jul 2019 15:50:38: start X-correlation... INFO @ Fri, 05 Jul 2019 15:50:38: end of X-cor INFO @ Fri, 05 Jul 2019 15:50:38: #2 finished! INFO @ Fri, 05 Jul 2019 15:50:38: #2 predicted fragment length is 180 bps INFO @ Fri, 05 Jul 2019 15:50:38: #2 alternative fragment length(s) may be 62,119,151,180,201,238,255,290,303,373,387,439,457,523,598 bps INFO @ Fri, 05 Jul 2019 15:50:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548167/ERX2548167.10_model.r pass1 - making usageList (14 chroms): 1 millis WARNING @ Fri, 05 Jul 2019 15:50:38: #2 Since the d (180) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:50:38: #2 You may need to consider one of the other alternative d(s): 62,119,151,180,201,238,255,290,303,373,387,439,457,523,598 WARNING @ Fri, 05 Jul 2019 15:50:38: #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 15:50:38: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:50:38: #3 Pre-compute pvalue-qvalue table... pass2 - checking and writing primary data (49 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 15:50:39: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:50:39: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548167/ERX2548167.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:50:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548167/ERX2548167.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:50:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548167/ERX2548167.10_summits.bed INFO @ Fri, 05 Jul 2019 15:50:39: Done! INFO @ Fri, 05 Jul 2019 15:50:39: #1 tag size is determined as 148 bps INFO @ Fri, 05 Jul 2019 15:50:39: #1 tag size = 148 INFO @ Fri, 05 Jul 2019 15:50:39: #1 total tags in treatment: 134551 INFO @ Fri, 05 Jul 2019 15:50:39: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:50:39: #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 15:50:39: #1 tags after filtering in treatment: 134551 INFO @ Fri, 05 Jul 2019 15:50:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:50:39: #1 finished! INFO @ Fri, 05 Jul 2019 15:50:39: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:50:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:50:39: #2 number of paired peaks: 242 WARNING @ Fri, 05 Jul 2019 15:50:39: Fewer paired peaks (242) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 242 pairs to build model! INFO @ Fri, 05 Jul 2019 15:50:39: start model_add_line... INFO @ Fri, 05 Jul 2019 15:50:39: start X-correlation... INFO @ Fri, 05 Jul 2019 15:50:39: end of X-cor INFO @ Fri, 05 Jul 2019 15:50:39: #2 finished! INFO @ Fri, 05 Jul 2019 15:50:39: #2 predicted fragment length is 180 bps INFO @ Fri, 05 Jul 2019 15:50:39: #2 alternative fragment length(s) may be 62,119,151,180,201,238,255,290,303,373,387,439,457,523,598 bps INFO @ Fri, 05 Jul 2019 15:50:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548167/ERX2548167.20_model.r pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (12 records, 4 fields): 1 millis WARNING @ Fri, 05 Jul 2019 15:50:39: #2 Since the d (180) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:50:39: #2 You may need to consider one of the other alternative d(s): 62,119,151,180,201,238,255,290,303,373,387,439,457,523,598 WARNING @ Fri, 05 Jul 2019 15:50:39: #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 15:50:39: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:50:39: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 15:50:40: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:50:40: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548167/ERX2548167.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:50:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548167/ERX2548167.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:50:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548167/ERX2548167.20_summits.bed INFO @ Fri, 05 Jul 2019 15:50:40: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis BigWig に変換しました。 CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling