Job ID = 2010064 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,194,743 reads read : 6,389,486 reads written : 3,194,743 reads 0-length : 3,194,743 rm: cannot remove ‘[DSE]RR*’: 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: 00:01:02 3194743 reads; of these: 3194743 (100.00%) were unpaired; of these: 126648 (3.96%) aligned 0 times 2612019 (81.76%) aligned exactly 1 time 456076 (14.28%) aligned >1 times 96.04% overall alignment rate Time searching: 00:01:02 Overall time: 00:01:02 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] 699132 / 3068095 = 0.2279 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 21:09:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2737658/SRX2737658.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2737658/SRX2737658.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2737658/SRX2737658.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2737658/SRX2737658.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 21:09:05: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:09:05: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:09:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2737658/SRX2737658.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2737658/SRX2737658.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2737658/SRX2737658.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2737658/SRX2737658.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 21:09:06: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:09:06: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:09:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2737658/SRX2737658.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2737658/SRX2737658.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2737658/SRX2737658.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2737658/SRX2737658.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 21:09:07: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:09:07: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:09:13: 1000000 INFO @ Fri, 05 Jul 2019 21:09:15: 1000000 INFO @ Fri, 05 Jul 2019 21:09:17: 1000000 INFO @ Fri, 05 Jul 2019 21:09:20: 2000000 INFO @ Fri, 05 Jul 2019 21:09:23: #1 tag size is determined as 101 bps INFO @ Fri, 05 Jul 2019 21:09:23: #1 tag size = 101 INFO @ Fri, 05 Jul 2019 21:09:23: #1 total tags in treatment: 2368963 INFO @ Fri, 05 Jul 2019 21:09:23: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:09:23: #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 21:09:23: #1 tags after filtering in treatment: 2368963 INFO @ Fri, 05 Jul 2019 21:09:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 21:09:23: #1 finished! INFO @ Fri, 05 Jul 2019 21:09:23: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:09:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:09:23: #2 number of paired peaks: 243 WARNING @ Fri, 05 Jul 2019 21:09:23: Fewer paired peaks (243) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 243 pairs to build model! INFO @ Fri, 05 Jul 2019 21:09:23: start model_add_line... INFO @ Fri, 05 Jul 2019 21:09:23: start X-correlation... INFO @ Fri, 05 Jul 2019 21:09:23: end of X-cor INFO @ Fri, 05 Jul 2019 21:09:23: #2 finished! INFO @ Fri, 05 Jul 2019 21:09:23: #2 predicted fragment length is 110 bps INFO @ Fri, 05 Jul 2019 21:09:23: #2 alternative fragment length(s) may be 110 bps INFO @ Fri, 05 Jul 2019 21:09:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2737658/SRX2737658.05_model.r WARNING @ Fri, 05 Jul 2019 21:09:23: #2 Since the d (110) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 21:09:23: #2 You may need to consider one of the other alternative d(s): 110 WARNING @ Fri, 05 Jul 2019 21:09:23: #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 21:09:23: #3 Call peaks... INFO @ Fri, 05 Jul 2019 21:09:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 21:09:24: 2000000 INFO @ Fri, 05 Jul 2019 21:09:27: 2000000 INFO @ Fri, 05 Jul 2019 21:09:28: #1 tag size is determined as 101 bps INFO @ Fri, 05 Jul 2019 21:09:28: #1 tag size = 101 INFO @ Fri, 05 Jul 2019 21:09:28: #1 total tags in treatment: 2368963 INFO @ Fri, 05 Jul 2019 21:09:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:09:28: #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 21:09:28: #1 tags after filtering in treatment: 2368963 INFO @ Fri, 05 Jul 2019 21:09:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 21:09:28: #1 finished! INFO @ Fri, 05 Jul 2019 21:09:28: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:09:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:09:28: #2 number of paired peaks: 243 WARNING @ Fri, 05 Jul 2019 21:09:28: Fewer paired peaks (243) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 243 pairs to build model! INFO @ Fri, 05 Jul 2019 21:09:28: start model_add_line... INFO @ Fri, 05 Jul 2019 21:09:28: start X-correlation... INFO @ Fri, 05 Jul 2019 21:09:28: end of X-cor INFO @ Fri, 05 Jul 2019 21:09:28: #2 finished! INFO @ Fri, 05 Jul 2019 21:09:28: #2 predicted fragment length is 110 bps INFO @ Fri, 05 Jul 2019 21:09:28: #2 alternative fragment length(s) may be 110 bps INFO @ Fri, 05 Jul 2019 21:09:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2737658/SRX2737658.10_model.r WARNING @ Fri, 05 Jul 2019 21:09:28: #2 Since the d (110) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 21:09:28: #2 You may need to consider one of the other alternative d(s): 110 WARNING @ Fri, 05 Jul 2019 21:09:28: #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 21:09:28: #3 Call peaks... INFO @ Fri, 05 Jul 2019 21:09:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 21:09:30: #1 tag size is determined as 101 bps INFO @ Fri, 05 Jul 2019 21:09:30: #1 tag size = 101 INFO @ Fri, 05 Jul 2019 21:09:30: #1 total tags in treatment: 2368963 INFO @ Fri, 05 Jul 2019 21:09:30: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:09:30: #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 21:09:30: #1 tags after filtering in treatment: 2368963 INFO @ Fri, 05 Jul 2019 21:09:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 21:09:30: #1 finished! INFO @ Fri, 05 Jul 2019 21:09:30: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:09:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:09:30: #2 number of paired peaks: 243 WARNING @ Fri, 05 Jul 2019 21:09:30: Fewer paired peaks (243) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 243 pairs to build model! INFO @ Fri, 05 Jul 2019 21:09:30: start model_add_line... INFO @ Fri, 05 Jul 2019 21:09:30: start X-correlation... INFO @ Fri, 05 Jul 2019 21:09:31: end of X-cor INFO @ Fri, 05 Jul 2019 21:09:31: #2 finished! INFO @ Fri, 05 Jul 2019 21:09:31: #2 predicted fragment length is 110 bps INFO @ Fri, 05 Jul 2019 21:09:31: #2 alternative fragment length(s) may be 110 bps INFO @ Fri, 05 Jul 2019 21:09:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2737658/SRX2737658.20_model.r WARNING @ Fri, 05 Jul 2019 21:09:31: #2 Since the d (110) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 21:09:31: #2 You may need to consider one of the other alternative d(s): 110 WARNING @ Fri, 05 Jul 2019 21:09:31: #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 21:09:31: #3 Call peaks... INFO @ Fri, 05 Jul 2019 21:09:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 21:09:31: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 21:09:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2737658/SRX2737658.05_peaks.xls INFO @ Fri, 05 Jul 2019 21:09:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2737658/SRX2737658.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 21:09:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2737658/SRX2737658.05_summits.bed INFO @ Fri, 05 Jul 2019 21:09:34: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (2347 records, 4 fields): 5 millis INFO @ Fri, 05 Jul 2019 21:09:35: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 21:09:38: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 21:09:38: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2737658/SRX2737658.10_peaks.xls INFO @ Fri, 05 Jul 2019 21:09:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2737658/SRX2737658.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 21:09:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2737658/SRX2737658.10_summits.bed INFO @ Fri, 05 Jul 2019 21:09:38: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (1380 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 21:09:41: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2737658/SRX2737658.20_peaks.xls INFO @ Fri, 05 Jul 2019 21:09:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2737658/SRX2737658.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 21:09:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2737658/SRX2737658.20_summits.bed INFO @ Fri, 05 Jul 2019 21:09:41: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (712 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。