Job ID = 2237049 sra ファイルのダウンロード中... Completed: 105319K bytes transferred in 5 seconds (165704K 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 --:--:-- --:--:-- --:--:-- 0 100 16380 0 16380 0 0 21941 0 --:--:-- --:--:-- --:--:-- 29460 100 37992 0 37992 0 0 50825 0 --:--:-- --:--:-- --:--:-- 68208 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 6438791 spots for /home/okishinya/chipatlas/results/ce10/SRX080104/SRR298924.sra Written 6438791 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: 00:00:39 6438791 reads; of these: 6438791 (100.00%) were unpaired; of these: 4596194 (71.38%) aligned 0 times 1528956 (23.75%) aligned exactly 1 time 313641 (4.87%) aligned >1 times 28.62% overall alignment rate Time searching: 00:00:39 Overall time: 00:00:39 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 290134 / 1842597 = 0.1575 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 @ Thu, 30 Apr 2015 11:26:07: # Command line: callpeak -t SRX080104.bam -f BAM -g ce -n SRX080104.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX080104.05 # format = BAM # ChIP-seq file = ['SRX080104.bam'] # control file = None # effective genome size = 9.00e+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 @ Thu, 30 Apr 2015 11:26:07: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:26:07: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:26:07: # Command line: callpeak -t SRX080104.bam -f BAM -g ce -n SRX080104.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX080104.10 # format = BAM # ChIP-seq file = ['SRX080104.bam'] # control file = None # effective genome size = 9.00e+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 @ Thu, 30 Apr 2015 11:26:07: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:26:07: # Command line: callpeak -t SRX080104.bam -f BAM -g ce -n SRX080104.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX080104.20 # format = BAM # ChIP-seq file = ['SRX080104.bam'] # control file = None # effective genome size = 9.00e+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 @ Thu, 30 Apr 2015 11:26:07: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:26:07: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:26:07: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:26:12: 1000000 INFO @ Thu, 30 Apr 2015 11:26:12: 1000000 INFO @ Thu, 30 Apr 2015 11:26:12: 1000000 INFO @ Thu, 30 Apr 2015 11:26:14: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:26:14: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:26:14: #1 total tags in treatment: 1552463 INFO @ Thu, 30 Apr 2015 11:26:14: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:26:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:26:14: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:26:14: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:26:14: #1 total tags in treatment: 1552463 INFO @ Thu, 30 Apr 2015 11:26:14: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:26:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:26:14: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:26:14: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:26:14: #1 total tags in treatment: 1552463 INFO @ Thu, 30 Apr 2015 11:26:14: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:26:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:26:15: #1 tags after filtering in treatment: 1552444 INFO @ Thu, 30 Apr 2015 11:26:15: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:26:15: #1 finished! INFO @ Thu, 30 Apr 2015 11:26:15: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:26:15: #1 tags after filtering in treatment: 1552444 INFO @ Thu, 30 Apr 2015 11:26:15: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:26:15: #1 finished! INFO @ Thu, 30 Apr 2015 11:26:15: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:26:15: #1 tags after filtering in treatment: 1552444 INFO @ Thu, 30 Apr 2015 11:26:15: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:26:15: #1 finished! INFO @ Thu, 30 Apr 2015 11:26:15: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:26:15: #2 number of paired peaks: 484 WARNING @ Thu, 30 Apr 2015 11:26:15: Fewer paired peaks (484) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 484 pairs to build model! INFO @ Thu, 30 Apr 2015 11:26:15: start model_add_line... INFO @ Thu, 30 Apr 2015 11:26:15: #2 number of paired peaks: 484 WARNING @ Thu, 30 Apr 2015 11:26:15: Fewer paired peaks (484) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 484 pairs to build model! INFO @ Thu, 30 Apr 2015 11:26:15: start model_add_line... INFO @ Thu, 30 Apr 2015 11:26:15: #2 number of paired peaks: 484 WARNING @ Thu, 30 Apr 2015 11:26:15: Fewer paired peaks (484) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 484 pairs to build model! INFO @ Thu, 30 Apr 2015 11:26:15: start model_add_line... INFO @ Thu, 30 Apr 2015 11:26:16: start X-correlation... INFO @ Thu, 30 Apr 2015 11:26:16: end of X-cor INFO @ Thu, 30 Apr 2015 11:26:16: #2 finished! INFO @ Thu, 30 Apr 2015 11:26:16: #2 predicted fragment length is 90 bps INFO @ Thu, 30 Apr 2015 11:26:16: #2 alternative fragment length(s) may be 37,90 bps INFO @ Thu, 30 Apr 2015 11:26:16: #2.2 Generate R script for model : SRX080104.05_model.r INFO @ Thu, 30 Apr 2015 11:26:16: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:26:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:26:16: start X-correlation... INFO @ Thu, 30 Apr 2015 11:26:16: end of X-cor INFO @ Thu, 30 Apr 2015 11:26:16: #2 finished! INFO @ Thu, 30 Apr 2015 11:26:16: #2 predicted fragment length is 90 bps INFO @ Thu, 30 Apr 2015 11:26:16: #2 alternative fragment length(s) may be 37,90 bps INFO @ Thu, 30 Apr 2015 11:26:16: #2.2 Generate R script for model : SRX080104.10_model.r INFO @ Thu, 30 Apr 2015 11:26:16: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:26:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:26:16: start X-correlation... INFO @ Thu, 30 Apr 2015 11:26:16: end of X-cor INFO @ Thu, 30 Apr 2015 11:26:16: #2 finished! INFO @ Thu, 30 Apr 2015 11:26:16: #2 predicted fragment length is 90 bps INFO @ Thu, 30 Apr 2015 11:26:16: #2 alternative fragment length(s) may be 37,90 bps INFO @ Thu, 30 Apr 2015 11:26:16: #2.2 Generate R script for model : SRX080104.20_model.r INFO @ Thu, 30 Apr 2015 11:26:16: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:26:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:26:25: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:26:26: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:26:26: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:26:32: #4 Write output xls file... SRX080104.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:26:32: #4 Write peak in narrowPeak format file... SRX080104.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:26:32: #4 Write summits bed file... SRX080104.20_summits.bed INFO @ Thu, 30 Apr 2015 11:26:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (54 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:26:32: #4 Write output xls file... SRX080104.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:26:32: #4 Write peak in narrowPeak format file... SRX080104.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:26:32: #4 Write summits bed file... SRX080104.05_summits.bed INFO @ Thu, 30 Apr 2015 11:26:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (462 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:26:33: #4 Write output xls file... SRX080104.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:26:33: #4 Write peak in narrowPeak format file... SRX080104.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:26:33: #4 Write summits bed file... SRX080104.10_summits.bed INFO @ Thu, 30 Apr 2015 11:26:33: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (192 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。