Job ID = 2007626 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,197,212 reads read : 11,197,212 reads written : 11,197,212 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529739.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: 00:04:53 11197212 reads; of these: 11197212 (100.00%) were unpaired; of these: 336214 (3.00%) aligned 0 times 8620917 (76.99%) aligned exactly 1 time 2240081 (20.01%) aligned >1 times 97.00% overall alignment rate Time searching: 00:04:53 Overall time: 00:04:53 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] 10785843 / 10860998 = 0.9931 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 16:09:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548228/ERX2548228.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548228/ERX2548228.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548228/ERX2548228.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548228/ERX2548228.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 16:09:28: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:09:28: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:09:28: #1 tag size is determined as 71 bps INFO @ Fri, 05 Jul 2019 16:09:28: #1 tag size = 71 INFO @ Fri, 05 Jul 2019 16:09:28: #1 total tags in treatment: 75155 INFO @ Fri, 05 Jul 2019 16:09:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:09:28: #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 16:09:28: #1 tags after filtering in treatment: 75155 INFO @ Fri, 05 Jul 2019 16:09:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:09:28: #1 finished! INFO @ Fri, 05 Jul 2019 16:09:28: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:09:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:09:28: #2 number of paired peaks: 453 WARNING @ Fri, 05 Jul 2019 16:09:28: Fewer paired peaks (453) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 453 pairs to build model! INFO @ Fri, 05 Jul 2019 16:09:28: start model_add_line... INFO @ Fri, 05 Jul 2019 16:09:28: start X-correlation... INFO @ Fri, 05 Jul 2019 16:09:28: end of X-cor INFO @ Fri, 05 Jul 2019 16:09:28: #2 finished! INFO @ Fri, 05 Jul 2019 16:09:28: #2 predicted fragment length is 69 bps INFO @ Fri, 05 Jul 2019 16:09:28: #2 alternative fragment length(s) may be 69,114,572,587 bps INFO @ Fri, 05 Jul 2019 16:09:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548228/ERX2548228.05_model.r INFO @ Fri, 05 Jul 2019 16:09:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548228/ERX2548228.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548228/ERX2548228.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548228/ERX2548228.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548228/ERX2548228.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 16:09:29: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:09:29: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:09:29: #1 tag size is determined as 71 bps INFO @ Fri, 05 Jul 2019 16:09:29: #1 tag size = 71 INFO @ Fri, 05 Jul 2019 16:09:29: #1 total tags in treatment: 75155 INFO @ Fri, 05 Jul 2019 16:09:29: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:09:29: #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 16:09:29: #1 tags after filtering in treatment: 75155 INFO @ Fri, 05 Jul 2019 16:09:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:09:29: #1 finished! INFO @ Fri, 05 Jul 2019 16:09:29: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:09:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:09:29: #2 number of paired peaks: 453 WARNING @ Fri, 05 Jul 2019 16:09:29: Fewer paired peaks (453) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 453 pairs to build model! INFO @ Fri, 05 Jul 2019 16:09:29: start model_add_line... INFO @ Fri, 05 Jul 2019 16:09:29: start X-correlation... INFO @ Fri, 05 Jul 2019 16:09:29: end of X-cor INFO @ Fri, 05 Jul 2019 16:09:29: #2 finished! INFO @ Fri, 05 Jul 2019 16:09:29: #2 predicted fragment length is 69 bps INFO @ Fri, 05 Jul 2019 16:09:29: #2 alternative fragment length(s) may be 69,114,572,587 bps INFO @ Fri, 05 Jul 2019 16:09:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548228/ERX2548228.10_model.r WARNING @ Fri, 05 Jul 2019 16:09:44: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:09:44: #2 You may need to consider one of the other alternative d(s): 69,114,572,587 WARNING @ Fri, 05 Jul 2019 16:09:44: #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 16:09:44: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:09:44: #3 Pre-compute pvalue-qvalue table... WARNING @ Fri, 05 Jul 2019 16:09:44: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:09:44: #2 You may need to consider one of the other alternative d(s): 69,114,572,587 WARNING @ Fri, 05 Jul 2019 16:09:44: #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 16:09:44: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:09:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:09:44: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:09:44: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:09:44: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548228/ERX2548228.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:09:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548228/ERX2548228.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:09:44: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548228/ERX2548228.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:09:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548228/ERX2548228.10_summits.bed INFO @ Fri, 05 Jul 2019 16:09:44: Done! INFO @ Fri, 05 Jul 2019 16:09:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548228/ERX2548228.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:09:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548228/ERX2548228.05_summits.bed INFO @ Fri, 05 Jul 2019 16:09:44: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (122 records, 4 fields): 2 millis pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (239 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 16:09:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548228/ERX2548228.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548228/ERX2548228.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548228/ERX2548228.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548228/ERX2548228.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 16:09:46: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:09:46: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:09:47: #1 tag size is determined as 71 bps INFO @ Fri, 05 Jul 2019 16:09:47: #1 tag size = 71 INFO @ Fri, 05 Jul 2019 16:09:47: #1 total tags in treatment: 75155 INFO @ Fri, 05 Jul 2019 16:09:47: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:09:47: #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 16:09:47: #1 tags after filtering in treatment: 75155 INFO @ Fri, 05 Jul 2019 16:09:47: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:09:47: #1 finished! INFO @ Fri, 05 Jul 2019 16:09:47: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:09:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:09:47: #2 number of paired peaks: 453 WARNING @ Fri, 05 Jul 2019 16:09:47: Fewer paired peaks (453) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 453 pairs to build model! INFO @ Fri, 05 Jul 2019 16:09:47: start model_add_line... INFO @ Fri, 05 Jul 2019 16:09:47: start X-correlation... INFO @ Fri, 05 Jul 2019 16:09:47: end of X-cor INFO @ Fri, 05 Jul 2019 16:09:47: #2 finished! INFO @ Fri, 05 Jul 2019 16:09:47: #2 predicted fragment length is 69 bps INFO @ Fri, 05 Jul 2019 16:09:47: #2 alternative fragment length(s) may be 69,114,572,587 bps INFO @ Fri, 05 Jul 2019 16:09:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548228/ERX2548228.20_model.r WARNING @ Fri, 05 Jul 2019 16:09:47: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:09:47: #2 You may need to consider one of the other alternative d(s): 69,114,572,587 WARNING @ Fri, 05 Jul 2019 16:09:47: #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 16:09:47: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:09:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:09:47: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:09:47: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548228/ERX2548228.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:09:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548228/ERX2548228.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:09:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548228/ERX2548228.20_summits.bed INFO @ Fri, 05 Jul 2019 16:09:47: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (70 records, 4 fields): 2 millis CompletedMACS2peakCalling