Job ID = 9037670 sra ファイルのダウンロード中... Completed: 302631K bytes transferred in 6 seconds (408071K 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 6903 0 6903 0 0 976 0 --:--:-- 0:00:07 --:--:-- 10443 100 31694 0 31694 0 0 3852 0 --:--:-- 0:00:08 --:--:-- 17385 100 44921 0 44921 0 0 5247 0 --:--:-- 0:00:08 --:--:-- 20854 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 14735796 spots for /home/okishinya/chipatlas/results/sacCer3/SRX977461/SRR1951307.sra Written 14735796 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: 00:01:56 14735796 reads; of these: 14735796 (100.00%) were unpaired; of these: 2302607 (15.63%) aligned 0 times 11110412 (75.40%) aligned exactly 1 time 1322777 (8.98%) aligned >1 times 84.37% overall alignment rate Time searching: 00:01:56 Overall time: 00:01:56 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] 12068261 / 12433189 = 0.9706 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 05:12:08: # Command line: callpeak -t SRX977461.bam -f BAM -g 12100000 -n SRX977461.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX977461.05 # format = BAM # ChIP-seq file = ['SRX977461.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 05:12:08: #1 read tag files... INFO @ Sun, 04 Jun 2017 05:12:08: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 05:12:08: # Command line: callpeak -t SRX977461.bam -f BAM -g 12100000 -n SRX977461.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX977461.10 # format = BAM # ChIP-seq file = ['SRX977461.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 05:12:08: #1 read tag files... INFO @ Sun, 04 Jun 2017 05:12:08: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 05:12:08: # Command line: callpeak -t SRX977461.bam -f BAM -g 12100000 -n SRX977461.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX977461.20 # format = BAM # ChIP-seq file = ['SRX977461.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 05:12:08: #1 read tag files... INFO @ Sun, 04 Jun 2017 05:12:08: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 05:12:10: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 05:12:10: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 05:12:10: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 05:12:10: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 05:12:10: #1 total tags in treatment: 364928 INFO @ Sun, 04 Jun 2017 05:12:10: #1 total tags in treatment: 364928 INFO @ Sun, 04 Jun 2017 05:12:10: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 05:12:10: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 05:12:10: #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 05:12:10: #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 05:12:10: #1 tags after filtering in treatment: 364540 INFO @ Sun, 04 Jun 2017 05:12:10: #1 tags after filtering in treatment: 364540 INFO @ Sun, 04 Jun 2017 05:12:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 05:12:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 05:12:10: #1 finished! INFO @ Sun, 04 Jun 2017 05:12:10: #1 finished! INFO @ Sun, 04 Jun 2017 05:12:10: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 05:12:10: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 05:12:10: #2 number of paired peaks: 491 WARNING @ Sun, 04 Jun 2017 05:12:10: Fewer paired peaks (491) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 491 pairs to build model! INFO @ Sun, 04 Jun 2017 05:12:10: #2 number of paired peaks: 491 WARNING @ Sun, 04 Jun 2017 05:12:10: Fewer paired peaks (491) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 491 pairs to build model! INFO @ Sun, 04 Jun 2017 05:12:10: start model_add_line... INFO @ Sun, 04 Jun 2017 05:12:10: start model_add_line... INFO @ Sun, 04 Jun 2017 05:12:10: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 05:12:10: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 05:12:10: #1 total tags in treatment: 364928 INFO @ Sun, 04 Jun 2017 05:12:10: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 05:12:10: #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 05:12:10: #1 tags after filtering in treatment: 364540 INFO @ Sun, 04 Jun 2017 05:12:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 05:12:10: #1 finished! INFO @ Sun, 04 Jun 2017 05:12:10: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 05:12:10: #2 number of paired peaks: 491 WARNING @ Sun, 04 Jun 2017 05:12:10: Fewer paired peaks (491) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 491 pairs to build model! INFO @ Sun, 04 Jun 2017 05:12:10: start model_add_line... INFO @ Sun, 04 Jun 2017 05:12:12: start X-correlation... INFO @ Sun, 04 Jun 2017 05:12:12: start X-correlation... INFO @ Sun, 04 Jun 2017 05:12:12: end of X-cor INFO @ Sun, 04 Jun 2017 05:12:12: #2 finished! INFO @ Sun, 04 Jun 2017 05:12:12: #2 predicted fragment length is 46 bps INFO @ Sun, 04 Jun 2017 05:12:12: #2 alternative fragment length(s) may be 4,46,63,86,155,497,543,545,586 bps INFO @ Sun, 04 Jun 2017 05:12:12: #2.2 Generate R script for model : SRX977461.05_model.r INFO @ Sun, 04 Jun 2017 05:12:12: end of X-cor INFO @ Sun, 04 Jun 2017 05:12:12: #2 finished! INFO @ Sun, 04 Jun 2017 05:12:12: #2 predicted fragment length is 46 bps INFO @ Sun, 04 Jun 2017 05:12:12: #2 alternative fragment length(s) may be 4,46,63,86,155,497,543,545,586 bps INFO @ Sun, 04 Jun 2017 05:12:12: #2.2 Generate R script for model : SRX977461.10_model.r WARNING @ Sun, 04 Jun 2017 05:12:12: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 05:12:12: #2 You may need to consider one of the other alternative d(s): 4,46,63,86,155,497,543,545,586 WARNING @ Sun, 04 Jun 2017 05:12:12: #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 05:12:12: #3 Call peaks... INFO @ Sun, 04 Jun 2017 05:12:12: #3 Pre-compute pvalue-qvalue table... WARNING @ Sun, 04 Jun 2017 05:12:12: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 05:12:12: #2 You may need to consider one of the other alternative d(s): 4,46,63,86,155,497,543,545,586 WARNING @ Sun, 04 Jun 2017 05:12:12: #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 05:12:12: #3 Call peaks... INFO @ Sun, 04 Jun 2017 05:12:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 05:12:12: start X-correlation... INFO @ Sun, 04 Jun 2017 05:12:12: end of X-cor INFO @ Sun, 04 Jun 2017 05:12:12: #2 finished! INFO @ Sun, 04 Jun 2017 05:12:12: #2 predicted fragment length is 46 bps INFO @ Sun, 04 Jun 2017 05:12:12: #2 alternative fragment length(s) may be 4,46,63,86,155,497,543,545,586 bps INFO @ Sun, 04 Jun 2017 05:12:12: #2.2 Generate R script for model : SRX977461.20_model.r WARNING @ Sun, 04 Jun 2017 05:12:12: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 05:12:12: #2 You may need to consider one of the other alternative d(s): 4,46,63,86,155,497,543,545,586 WARNING @ Sun, 04 Jun 2017 05:12:12: #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 05:12:12: #3 Call peaks... INFO @ Sun, 04 Jun 2017 05:12:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 05:12:14: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 05:12:14: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 05:12:14: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 04 Jun 2017 05:12:16: #4 Write output xls file... SRX977461.10_peaks.xls INFO @ Sun, 04 Jun 2017 05:12:16: #4 Write peak in narrowPeak format file... SRX977461.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 05:12:16: #4 Write summits bed file... SRX977461.10_summits.bed INFO @ Sun, 04 Jun 2017 05:12:16: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (90 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 05:12:16: #4 Write output xls file... SRX977461.05_peaks.xls INFO @ Sun, 04 Jun 2017 05:12:16: #4 Write peak in narrowPeak format file... SRX977461.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 05:12:16: #4 Write summits bed file... SRX977461.05_summits.bed INFO @ Sun, 04 Jun 2017 05:12:16: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (342 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 05:12:16: #4 Write output xls file... SRX977461.20_peaks.xls INFO @ Sun, 04 Jun 2017 05:12:16: #4 Write peak in narrowPeak format file... SRX977461.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 05:12:16: #4 Write summits bed file... SRX977461.20_summits.bed INFO @ Sun, 04 Jun 2017 05:12:16: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (6 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。