Job ID = 9037659 sra ファイルのダウンロード中... Completed: 95993K bytes transferred in 4 seconds (187641K bits/sec), in 1 file, 2 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 100 14324 0 14324 0 0 1940 0 --:--:-- 0:00:07 --:--:-- 14527 100 38318 0 38318 0 0 4574 0 --:--:-- 0:00:08 --:--:-- 19323 100 54467 0 54467 0 0 6024 0 --:--:-- 0:00:09 --:--:-- 20592 sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Written 2791302 spots for /home/okishinya/chipatlas/results/sacCer3/SRX977450/SRR1951296.sra Written 2791302 spots total rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません 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: 00:01:00 2791302 reads; of these: 2791302 (100.00%) were unpaired; of these: 1195672 (42.84%) aligned 0 times 330752 (11.85%) aligned exactly 1 time 1264878 (45.31%) aligned >1 times 57.16% overall alignment rate Time searching: 00:01:00 Overall time: 00:01:00 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] 1383834 / 1595630 = 0.8673 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 @ Sun, 04 Jun 2017 05:07:11: # Command line: callpeak -t SRX977450.bam -f BAM -g 12100000 -n SRX977450.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX977450.20 # format = BAM # ChIP-seq file = ['SRX977450.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 INFO @ Sun, 04 Jun 2017 05:07:11: #1 read tag files... INFO @ Sun, 04 Jun 2017 05:07:11: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 05:07:11: # Command line: callpeak -t SRX977450.bam -f BAM -g 12100000 -n SRX977450.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX977450.10 # format = BAM # ChIP-seq file = ['SRX977450.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 INFO @ Sun, 04 Jun 2017 05:07:11: #1 read tag files... INFO @ Sun, 04 Jun 2017 05:07:11: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 05:07:11: # Command line: callpeak -t SRX977450.bam -f BAM -g 12100000 -n SRX977450.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX977450.05 # format = BAM # ChIP-seq file = ['SRX977450.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 INFO @ Sun, 04 Jun 2017 05:07:11: #1 read tag files... INFO @ Sun, 04 Jun 2017 05:07:11: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 05:07:12: #1 tag size is determined as 45 bps INFO @ Sun, 04 Jun 2017 05:07:12: #1 tag size = 45 INFO @ Sun, 04 Jun 2017 05:07:12: #1 total tags in treatment: 211796 INFO @ Sun, 04 Jun 2017 05:07:12: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 05:07:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 05:07:12: #1 tag size is determined as 45 bps INFO @ Sun, 04 Jun 2017 05:07:12: #1 tag size = 45 INFO @ Sun, 04 Jun 2017 05:07:12: #1 total tags in treatment: 211796 INFO @ Sun, 04 Jun 2017 05:07:12: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 05:07:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 05:07:12: #1 tag size is determined as 45 bps INFO @ Sun, 04 Jun 2017 05:07:12: #1 tag size = 45 INFO @ Sun, 04 Jun 2017 05:07:12: #1 total tags in treatment: 211796 INFO @ Sun, 04 Jun 2017 05:07:12: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 05:07:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 05:07:12: #1 tags after filtering in treatment: 210850 INFO @ Sun, 04 Jun 2017 05:07:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 05:07:12: #1 finished! INFO @ Sun, 04 Jun 2017 05:07:12: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 05:07:12: #1 tags after filtering in treatment: 210850 INFO @ Sun, 04 Jun 2017 05:07:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 05:07:12: #1 finished! INFO @ Sun, 04 Jun 2017 05:07:12: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 05:07:12: #1 tags after filtering in treatment: 210850 INFO @ Sun, 04 Jun 2017 05:07:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 05:07:12: #1 finished! INFO @ Sun, 04 Jun 2017 05:07:12: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 05:07:12: #2 number of paired peaks: 277 WARNING @ Sun, 04 Jun 2017 05:07:12: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Sun, 04 Jun 2017 05:07:12: start model_add_line... INFO @ Sun, 04 Jun 2017 05:07:12: #2 number of paired peaks: 277 WARNING @ Sun, 04 Jun 2017 05:07:12: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Sun, 04 Jun 2017 05:07:12: start model_add_line... INFO @ Sun, 04 Jun 2017 05:07:12: #2 number of paired peaks: 277 WARNING @ Sun, 04 Jun 2017 05:07:12: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Sun, 04 Jun 2017 05:07:12: start model_add_line... INFO @ Sun, 04 Jun 2017 05:07:13: start X-correlation... INFO @ Sun, 04 Jun 2017 05:07:13: end of X-cor INFO @ Sun, 04 Jun 2017 05:07:13: #2 finished! INFO @ Sun, 04 Jun 2017 05:07:13: #2 predicted fragment length is 38 bps INFO @ Sun, 04 Jun 2017 05:07:13: #2 alternative fragment length(s) may be 38 bps INFO @ Sun, 04 Jun 2017 05:07:13: #2.2 Generate R script for model : SRX977450.10_model.r WARNING @ Sun, 04 Jun 2017 05:07:13: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 05:07:13: #2 You may need to consider one of the other alternative d(s): 38 WARNING @ Sun, 04 Jun 2017 05:07:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Jun 2017 05:07:13: #3 Call peaks... INFO @ Sun, 04 Jun 2017 05:07:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 05:07:13: start X-correlation... INFO @ Sun, 04 Jun 2017 05:07:13: start X-correlation... INFO @ Sun, 04 Jun 2017 05:07:13: end of X-cor INFO @ Sun, 04 Jun 2017 05:07:13: #2 finished! INFO @ Sun, 04 Jun 2017 05:07:13: #2 predicted fragment length is 38 bps INFO @ Sun, 04 Jun 2017 05:07:13: #2 alternative fragment length(s) may be 38 bps INFO @ Sun, 04 Jun 2017 05:07:13: #2.2 Generate R script for model : SRX977450.20_model.r INFO @ Sun, 04 Jun 2017 05:07:13: end of X-cor INFO @ Sun, 04 Jun 2017 05:07:13: #2 finished! INFO @ Sun, 04 Jun 2017 05:07:13: #2 predicted fragment length is 38 bps INFO @ Sun, 04 Jun 2017 05:07:13: #2 alternative fragment length(s) may be 38 bps INFO @ Sun, 04 Jun 2017 05:07:13: #2.2 Generate R script for model : SRX977450.05_model.r WARNING @ Sun, 04 Jun 2017 05:07:13: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 05:07:13: #2 You may need to consider one of the other alternative d(s): 38 WARNING @ Sun, 04 Jun 2017 05:07:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Jun 2017 05:07:13: #3 Call peaks... INFO @ Sun, 04 Jun 2017 05:07:13: #3 Pre-compute pvalue-qvalue table... WARNING @ Sun, 04 Jun 2017 05:07:13: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 05:07:13: #2 You may need to consider one of the other alternative d(s): 38 WARNING @ Sun, 04 Jun 2017 05:07:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Jun 2017 05:07:13: #3 Call peaks... INFO @ Sun, 04 Jun 2017 05:07:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 05:07:14: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 05:07:14: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 05:07:14: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 05:07:15: #4 Write output xls file... SRX977450.10_peaks.xls INFO @ Sun, 04 Jun 2017 05:07:15: #4 Write peak in narrowPeak format file... SRX977450.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 05:07:15: #4 Write output xls file... SRX977450.20_peaks.xls INFO @ Sun, 04 Jun 2017 05:07:15: #4 Write summits bed file... SRX977450.10_summits.bed INFO @ Sun, 04 Jun 2017 05:07:15: Done! INFO @ Sun, 04 Jun 2017 05:07:15: #4 Write peak in narrowPeak format file... SRX977450.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 05:07:15: #4 Write summits bed file... SRX977450.20_summits.bed INFO @ Sun, 04 Jun 2017 05:07:15: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (390 records, 4 fields): 2 millis pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (237 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 04 Jun 2017 05:07:15: #4 Write output xls file... SRX977450.05_peaks.xls INFO @ Sun, 04 Jun 2017 05:07:15: #4 Write peak in narrowPeak format file... SRX977450.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 05:07:15: #4 Write summits bed file... SRX977450.05_summits.bed INFO @ Sun, 04 Jun 2017 05:07:15: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (636 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。