Job ID = 2006323 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,559,183 reads read : 2,559,183 reads written : 2,559,183 spots read : 2,464,775 reads read : 2,464,775 reads written : 2,464,775 spots read : 2,519,097 reads read : 2,519,097 reads written : 2,519,097 spots read : 2,423,840 reads read : 2,423,840 reads written : 2,423,840 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529490.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529491.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529492.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: 00:02:38 9966895 reads; of these: 9966895 (100.00%) were unpaired; of these: 437001 (4.38%) aligned 0 times 8056051 (80.83%) aligned exactly 1 time 1473843 (14.79%) aligned >1 times 95.62% overall alignment rate Time searching: 00:02:38 Overall time: 00:02:38 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] 9075526 / 9529894 = 0.9523 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 15:48:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548156/ERX2548156.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548156/ERX2548156.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548156/ERX2548156.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548156/ERX2548156.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 15:48:05: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:48:05: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:48:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548156/ERX2548156.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548156/ERX2548156.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548156/ERX2548156.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548156/ERX2548156.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 15:48:06: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:48:06: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:48:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548156/ERX2548156.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548156/ERX2548156.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548156/ERX2548156.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548156/ERX2548156.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 15:48:07: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:48:07: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:48:10: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:48:10: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:48:10: #1 total tags in treatment: 454368 INFO @ Fri, 05 Jul 2019 15:48:10: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:48:10: #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 15:48:10: #1 tags after filtering in treatment: 454368 INFO @ Fri, 05 Jul 2019 15:48:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:48:10: #1 finished! INFO @ Fri, 05 Jul 2019 15:48:10: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:48:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:48:11: #2 number of paired peaks: 544 WARNING @ Fri, 05 Jul 2019 15:48:11: Fewer paired peaks (544) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 544 pairs to build model! INFO @ Fri, 05 Jul 2019 15:48:11: start model_add_line... INFO @ Fri, 05 Jul 2019 15:48:11: start X-correlation... INFO @ Fri, 05 Jul 2019 15:48:11: end of X-cor INFO @ Fri, 05 Jul 2019 15:48:11: #2 finished! INFO @ Fri, 05 Jul 2019 15:48:11: #2 predicted fragment length is 148 bps INFO @ Fri, 05 Jul 2019 15:48:11: #2 alternative fragment length(s) may be 148 bps INFO @ Fri, 05 Jul 2019 15:48:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548156/ERX2548156.05_model.r WARNING @ Fri, 05 Jul 2019 15:48:11: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:48:11: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Fri, 05 Jul 2019 15:48:11: #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 15:48:11: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:48:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:48:12: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:48:12: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:48:12: #1 total tags in treatment: 454368 INFO @ Fri, 05 Jul 2019 15:48:12: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:48:12: #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 15:48:12: #1 tags after filtering in treatment: 454368 INFO @ Fri, 05 Jul 2019 15:48:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:48:12: #1 finished! INFO @ Fri, 05 Jul 2019 15:48:12: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:48:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:48:12: #2 number of paired peaks: 544 WARNING @ Fri, 05 Jul 2019 15:48:12: Fewer paired peaks (544) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 544 pairs to build model! INFO @ Fri, 05 Jul 2019 15:48:12: start model_add_line... INFO @ Fri, 05 Jul 2019 15:48:12: start X-correlation... INFO @ Fri, 05 Jul 2019 15:48:12: end of X-cor INFO @ Fri, 05 Jul 2019 15:48:12: #2 finished! INFO @ Fri, 05 Jul 2019 15:48:12: #2 predicted fragment length is 148 bps INFO @ Fri, 05 Jul 2019 15:48:12: #2 alternative fragment length(s) may be 148 bps INFO @ Fri, 05 Jul 2019 15:48:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548156/ERX2548156.10_model.r WARNING @ Fri, 05 Jul 2019 15:48:12: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:48:12: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Fri, 05 Jul 2019 15:48:12: #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 15:48:12: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:48:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:48:13: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:48:13: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:48:13: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:48:13: #1 total tags in treatment: 454368 INFO @ Fri, 05 Jul 2019 15:48:13: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:48:13: #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 15:48:13: #1 tags after filtering in treatment: 454368 INFO @ Fri, 05 Jul 2019 15:48:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:48:13: #1 finished! INFO @ Fri, 05 Jul 2019 15:48:13: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:48:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:48:13: #2 number of paired peaks: 544 WARNING @ Fri, 05 Jul 2019 15:48:13: Fewer paired peaks (544) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 544 pairs to build model! INFO @ Fri, 05 Jul 2019 15:48:13: start model_add_line... INFO @ Fri, 05 Jul 2019 15:48:13: start X-correlation... INFO @ Fri, 05 Jul 2019 15:48:13: end of X-cor INFO @ Fri, 05 Jul 2019 15:48:13: #2 finished! INFO @ Fri, 05 Jul 2019 15:48:13: #2 predicted fragment length is 148 bps INFO @ Fri, 05 Jul 2019 15:48:13: #2 alternative fragment length(s) may be 148 bps INFO @ Fri, 05 Jul 2019 15:48:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548156/ERX2548156.20_model.r WARNING @ Fri, 05 Jul 2019 15:48:13: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:48:13: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Fri, 05 Jul 2019 15:48:13: #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 15:48:13: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:48:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:48:13: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548156/ERX2548156.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:48:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548156/ERX2548156.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:48:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548156/ERX2548156.05_summits.bed INFO @ Fri, 05 Jul 2019 15:48:13: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (317 records, 4 fields): 4 millis INFO @ Fri, 05 Jul 2019 15:48:14: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:48:14: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548156/ERX2548156.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:48:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548156/ERX2548156.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:48:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548156/ERX2548156.10_summits.bed INFO @ Fri, 05 Jul 2019 15:48:14: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (199 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 15:48:15: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:48:15: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548156/ERX2548156.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:48:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548156/ERX2548156.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:48:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548156/ERX2548156.20_summits.bed INFO @ Fri, 05 Jul 2019 15:48:15: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (108 records, 4 fields): 2 millis BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling BigWig に変換しました。