Job ID = 2006290 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,671,327 reads read : 2,671,327 reads written : 2,671,327 spots read : 2,571,838 reads read : 2,571,838 reads written : 2,571,838 spots read : 2,640,149 reads read : 2,640,149 reads written : 2,640,149 spots read : 2,480,084 reads read : 2,480,084 reads written : 2,480,084 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529440.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529441.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529443.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: 00:02:57 10363398 reads; of these: 10363398 (100.00%) were unpaired; of these: 780368 (7.53%) aligned 0 times 7913644 (76.36%) aligned exactly 1 time 1669386 (16.11%) aligned >1 times 92.47% overall alignment rate Time searching: 00:02:57 Overall time: 00:02:57 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] 9364777 / 9583030 = 0.9772 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 15:32:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548139/ERX2548139.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548139/ERX2548139.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548139/ERX2548139.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548139/ERX2548139.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 15:32:10: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:32:10: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:32:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548139/ERX2548139.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548139/ERX2548139.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548139/ERX2548139.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548139/ERX2548139.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 15:32:10: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:32:10: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:32:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548139/ERX2548139.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548139/ERX2548139.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548139/ERX2548139.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548139/ERX2548139.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 15:32:12: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:32:12: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:32:13: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:32:13: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:32:13: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:32:13: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:32:13: #1 total tags in treatment: 218253 INFO @ Fri, 05 Jul 2019 15:32:13: #1 total tags in treatment: 218253 INFO @ Fri, 05 Jul 2019 15:32:13: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:32:13: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:32:13: #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 15:32:13: #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 15:32:13: #1 tags after filtering in treatment: 218253 INFO @ Fri, 05 Jul 2019 15:32:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:32:13: #1 finished! INFO @ Fri, 05 Jul 2019 15:32:13: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:32:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:32:13: #1 tags after filtering in treatment: 218253 INFO @ Fri, 05 Jul 2019 15:32:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:32:13: #1 finished! INFO @ Fri, 05 Jul 2019 15:32:13: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:32:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:32:13: #2 number of paired peaks: 487 WARNING @ Fri, 05 Jul 2019 15:32:13: Fewer paired peaks (487) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 487 pairs to build model! INFO @ Fri, 05 Jul 2019 15:32:13: start model_add_line... INFO @ Fri, 05 Jul 2019 15:32:13: start X-correlation... INFO @ Fri, 05 Jul 2019 15:32:13: #2 number of paired peaks: 487 WARNING @ Fri, 05 Jul 2019 15:32:13: Fewer paired peaks (487) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 487 pairs to build model! INFO @ Fri, 05 Jul 2019 15:32:13: start model_add_line... INFO @ Fri, 05 Jul 2019 15:32:13: start X-correlation... INFO @ Fri, 05 Jul 2019 15:32:13: end of X-cor INFO @ Fri, 05 Jul 2019 15:32:13: #2 finished! INFO @ Fri, 05 Jul 2019 15:32:13: #2 predicted fragment length is 124 bps INFO @ Fri, 05 Jul 2019 15:32:13: #2 alternative fragment length(s) may be 4,63,68,124,144,155,181,195,472,491,531,561,580 bps INFO @ Fri, 05 Jul 2019 15:32:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548139/ERX2548139.10_model.r WARNING @ Fri, 05 Jul 2019 15:32:13: #2 Since the d (124) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:32:13: #2 You may need to consider one of the other alternative d(s): 4,63,68,124,144,155,181,195,472,491,531,561,580 WARNING @ Fri, 05 Jul 2019 15:32:13: #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 15:32:13: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:32:13: end of X-cor INFO @ Fri, 05 Jul 2019 15:32:13: #2 finished! INFO @ Fri, 05 Jul 2019 15:32:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:32:13: #2 predicted fragment length is 124 bps INFO @ Fri, 05 Jul 2019 15:32:13: #2 alternative fragment length(s) may be 4,63,68,124,144,155,181,195,472,491,531,561,580 bps INFO @ Fri, 05 Jul 2019 15:32:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548139/ERX2548139.05_model.r WARNING @ Fri, 05 Jul 2019 15:32:13: #2 Since the d (124) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:32:13: #2 You may need to consider one of the other alternative d(s): 4,63,68,124,144,155,181,195,472,491,531,561,580 WARNING @ Fri, 05 Jul 2019 15:32:13: #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 15:32:13: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:32:13: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 15:32:14: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:32:14: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 15:32:14: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548139/ERX2548139.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:32:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548139/ERX2548139.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:32:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548139/ERX2548139.10_summits.bed INFO @ Fri, 05 Jul 2019 15:32:15: Done! INFO @ Fri, 05 Jul 2019 15:32:15: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548139/ERX2548139.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:32:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548139/ERX2548139.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:32:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548139/ERX2548139.05_summits.bed INFO @ Fri, 05 Jul 2019 15:32:15: Done! pass1 - making usageList (16 chroms)INFO @ Fri, 05 Jul 2019 15:32:15: #1 tag size is determined as 75 bps : 0 millis pass1 - making usageList (16 chroms): 1 millis INFO @ Fri, 05 Jul 2019 15:32:18: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:32:18: #1 total tags in treatment: 218253 INFO @ Fri, 05 Jul 2019 15:32:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:32:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass2 - checking and writing primary data (117 records, 4 fields)pass2 - checking and writing primary data (52 records, 4 fields): 3142 millis : 1841 millis INFO @ Fri, 05 Jul 2019 15:32:18: #1 tags after filtering in treatment: 218253 INFO @ Fri, 05 Jul 2019 15:32:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:32:18: #1 finished! INFO @ Fri, 05 Jul 2019 15:32:18: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:32:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:32:18: #2 number of paired peaks: 487 WARNING @ Fri, 05 Jul 2019 15:32:18: Fewer paired peaks (487) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 487 pairs to build model! INFO @ Fri, 05 Jul 2019 15:32:18: start model_add_line... INFO @ Fri, 05 Jul 2019 15:32:18: start X-correlation... INFO @ Fri, 05 Jul 2019 15:32:18: end of X-cor INFO @ Fri, 05 Jul 2019 15:32:18: #2 finished! INFO @ Fri, 05 Jul 2019 15:32:18: #2 predicted fragment length is 124 bps INFO @ Fri, 05 Jul 2019 15:32:18: #2 alternative fragment length(s) may be 4,63,68,124,144,155,181,195,472,491,531,561,580 bps INFO @ Fri, 05 Jul 2019 15:32:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548139/ERX2548139.20_model.r WARNING @ Fri, 05 Jul 2019 15:32:18: #2 Since the d (124) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:32:18: #2 You may need to consider one of the other alternative d(s): 4,63,68,124,144,155,181,195,472,491,531,561,580 WARNING @ Fri, 05 Jul 2019 15:32:18: #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 15:32:18: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:32:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:32:19: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:32:21: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548139/ERX2548139.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:32:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548139/ERX2548139.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:32:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548139/ERX2548139.20_summits.bed INFO @ Fri, 05 Jul 2019 15:32:21: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (20 records, 4 fields): 1 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling