Job ID = 3001482 sra ファイルのダウンロード中... Completed: 2085166K bytes transferred in 28 seconds (604015K 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 40598 0 40598 0 0 42852 0 --:--:-- --:--:-- --:--:-- 53701 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 8444506 spots for /home/okishinya/chipatlas/results/ce10/SRX003825/SRR015065.sra Written 8444506 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:44 8444506 reads; of these: 8444506 (100.00%) were unpaired; of these: 7092309 (83.99%) aligned 0 times 1101790 (13.05%) aligned exactly 1 time 250407 (2.97%) aligned >1 times 16.01% overall alignment rate Time searching: 00:00:45 Overall time: 00:00:45 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] 73907 / 1352197 = 0.0547 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 @ Mon, 07 Sep 2015 18:46:07: # Command line: callpeak -t SRX003825.bam -f BAM -g ce -n SRX003825.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX003825.05 # format = BAM # ChIP-seq file = ['SRX003825.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 @ Mon, 07 Sep 2015 18:46:07: # Command line: callpeak -t SRX003825.bam -f BAM -g ce -n SRX003825.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX003825.20 # format = BAM # ChIP-seq file = ['SRX003825.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 @ Mon, 07 Sep 2015 18:46:07: # Command line: callpeak -t SRX003825.bam -f BAM -g ce -n SRX003825.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX003825.10 # format = BAM # ChIP-seq file = ['SRX003825.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 @ Mon, 07 Sep 2015 18:46:07: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:46:07: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:46:07: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:46:07: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:46:07: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:46:07: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:46:13: 1000000 INFO @ Mon, 07 Sep 2015 18:46:14: 1000000 INFO @ Mon, 07 Sep 2015 18:46:14: 1000000 INFO @ Mon, 07 Sep 2015 18:46:14: #1 tag size is determined as 37 bps INFO @ Mon, 07 Sep 2015 18:46:14: #1 tag size = 37 INFO @ Mon, 07 Sep 2015 18:46:14: #1 total tags in treatment: 1278290 INFO @ Mon, 07 Sep 2015 18:46:14: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:46:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 Sep 2015 18:46:15: #1 tags after filtering in treatment: 1278178 INFO @ Mon, 07 Sep 2015 18:46:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:46:15: #1 finished! INFO @ Mon, 07 Sep 2015 18:46:15: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:46:15: #2 number of paired peaks: 1379 INFO @ Mon, 07 Sep 2015 18:46:15: start model_add_line... INFO @ Mon, 07 Sep 2015 18:46:16: #1 tag size is determined as 37 bps INFO @ Mon, 07 Sep 2015 18:46:16: #1 tag size is determined as 37 bps INFO @ Mon, 07 Sep 2015 18:46:16: #1 tag size = 37 INFO @ Mon, 07 Sep 2015 18:46:16: #1 tag size = 37 INFO @ Mon, 07 Sep 2015 18:46:16: #1 total tags in treatment: 1278290 INFO @ Mon, 07 Sep 2015 18:46:16: #1 total tags in treatment: 1278290 INFO @ Mon, 07 Sep 2015 18:46:16: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:46:16: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:46:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 Sep 2015 18:46:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 Sep 2015 18:46:16: #1 tags after filtering in treatment: 1278178 INFO @ Mon, 07 Sep 2015 18:46:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:46:16: #1 finished! INFO @ Mon, 07 Sep 2015 18:46:16: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:46:16: #1 tags after filtering in treatment: 1278178 INFO @ Mon, 07 Sep 2015 18:46:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:46:16: #1 finished! INFO @ Mon, 07 Sep 2015 18:46:16: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:46:16: #2 number of paired peaks: 1379 INFO @ Mon, 07 Sep 2015 18:46:16: start model_add_line... INFO @ Mon, 07 Sep 2015 18:46:16: #2 number of paired peaks: 1379 INFO @ Mon, 07 Sep 2015 18:46:16: start model_add_line... INFO @ Mon, 07 Sep 2015 18:46:17: start X-correlation... INFO @ Mon, 07 Sep 2015 18:46:17: end of X-cor INFO @ Mon, 07 Sep 2015 18:46:17: #2 finished! INFO @ Mon, 07 Sep 2015 18:46:17: #2 predicted fragment length is 81 bps INFO @ Mon, 07 Sep 2015 18:46:17: #2 alternative fragment length(s) may be 81 bps INFO @ Mon, 07 Sep 2015 18:46:17: #2.2 Generate R script for model : SRX003825.05_model.r INFO @ Mon, 07 Sep 2015 18:46:17: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:46:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:46:18: start X-correlation... INFO @ Mon, 07 Sep 2015 18:46:18: end of X-cor INFO @ Mon, 07 Sep 2015 18:46:18: #2 finished! INFO @ Mon, 07 Sep 2015 18:46:18: #2 predicted fragment length is 81 bps INFO @ Mon, 07 Sep 2015 18:46:18: #2 alternative fragment length(s) may be 81 bps INFO @ Mon, 07 Sep 2015 18:46:18: #2.2 Generate R script for model : SRX003825.20_model.r INFO @ Mon, 07 Sep 2015 18:46:18: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:46:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:46:18: start X-correlation... INFO @ Mon, 07 Sep 2015 18:46:18: end of X-cor INFO @ Mon, 07 Sep 2015 18:46:18: #2 finished! INFO @ Mon, 07 Sep 2015 18:46:18: #2 predicted fragment length is 81 bps INFO @ Mon, 07 Sep 2015 18:46:18: #2 alternative fragment length(s) may be 81 bps INFO @ Mon, 07 Sep 2015 18:46:18: #2.2 Generate R script for model : SRX003825.10_model.r INFO @ Mon, 07 Sep 2015 18:46:18: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:46:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:46:25: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:46:26: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:46:27: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:46:31: #4 Write output xls file... SRX003825.05_peaks.xls INFO @ Mon, 07 Sep 2015 18:46:31: #4 Write peak in narrowPeak format file... SRX003825.05_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:46:31: #4 Write summits bed file... SRX003825.05_summits.bed INFO @ Mon, 07 Sep 2015 18:46:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1364 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:46:32: #4 Write output xls file... SRX003825.20_peaks.xls INFO @ Mon, 07 Sep 2015 18:46:32: #4 Write peak in narrowPeak format file... SRX003825.20_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:46:32: #4 Write summits bed file... SRX003825.20_summits.bed INFO @ Mon, 07 Sep 2015 18:46:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (216 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:46:33: #4 Write output xls file... SRX003825.10_peaks.xls INFO @ Mon, 07 Sep 2015 18:46:33: #4 Write peak in narrowPeak format file... SRX003825.10_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:46:33: #4 Write summits bed file... SRX003825.10_summits.bed INFO @ Mon, 07 Sep 2015 18:46:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (541 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。