Job ID = 2237074 sra ファイルのダウンロード中... Completed: 136806K bytes transferred in 6 seconds (176645K 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 --:--:-- --:--:-- --:--:-- 0 108 1087 0 1087 0 0 1951 0 --:--:-- --:--:-- --:--:-- 2969 100 36842 0 36842 0 0 49334 0 --:--:-- --:--:-- --:--:-- 66262 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 7097223 spots for /home/okishinya/chipatlas/results/ce10/SRX113616/SRR393716.sra Written 7097223 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: 00:02:00 7097223 reads; of these: 7097223 (100.00%) were unpaired; of these: 307217 (4.33%) aligned 0 times 4758376 (67.05%) aligned exactly 1 time 2031630 (28.63%) aligned >1 times 95.67% overall alignment rate Time searching: 00:02:00 Overall time: 00:02:00 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 2051670 / 6790006 = 0.3022 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 11:29:52: # Command line: callpeak -t SRX113616.bam -f BAM -g ce -n SRX113616.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX113616.05 # format = BAM # ChIP-seq file = ['SRX113616.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 11:29:52: # Command line: callpeak -t SRX113616.bam -f BAM -g ce -n SRX113616.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX113616.20 # format = BAM # ChIP-seq file = ['SRX113616.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 11:29:52: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:29:52: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:29:52: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:29:52: # Command line: callpeak -t SRX113616.bam -f BAM -g ce -n SRX113616.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX113616.10 # format = BAM # ChIP-seq file = ['SRX113616.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 11:29:52: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:29:52: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:29:52: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:29:58: 1000000 INFO @ Thu, 30 Apr 2015 11:29:58: 1000000 INFO @ Thu, 30 Apr 2015 11:29:58: 1000000 INFO @ Thu, 30 Apr 2015 11:30:03: 2000000 INFO @ Thu, 30 Apr 2015 11:30:03: 2000000 INFO @ Thu, 30 Apr 2015 11:30:04: 2000000 INFO @ Thu, 30 Apr 2015 11:30:09: 3000000 INFO @ Thu, 30 Apr 2015 11:30:09: 3000000 INFO @ Thu, 30 Apr 2015 11:30:10: 3000000 INFO @ Thu, 30 Apr 2015 11:30:14: 4000000 INFO @ Thu, 30 Apr 2015 11:30:16: 4000000 INFO @ Thu, 30 Apr 2015 11:30:17: 4000000 INFO @ Thu, 30 Apr 2015 11:30:18: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:30:18: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:30:18: #1 total tags in treatment: 4738336 INFO @ Thu, 30 Apr 2015 11:30:18: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:30:18: #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 11:30:19: #1 tags after filtering in treatment: 4719423 INFO @ Thu, 30 Apr 2015 11:30:19: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:30:19: #1 finished! INFO @ Thu, 30 Apr 2015 11:30:19: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:30:20: #2 number of paired peaks: 3984 INFO @ Thu, 30 Apr 2015 11:30:20: start model_add_line... INFO @ Thu, 30 Apr 2015 11:30:20: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:30:20: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:30:20: #1 total tags in treatment: 4738336 INFO @ Thu, 30 Apr 2015 11:30:20: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:30:20: #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 11:30:21: #1 tags after filtering in treatment: 4719423 INFO @ Thu, 30 Apr 2015 11:30:21: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:30:21: #1 finished! INFO @ Thu, 30 Apr 2015 11:30:21: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:30:22: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:30:22: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:30:22: #1 total tags in treatment: 4738336 INFO @ Thu, 30 Apr 2015 11:30:22: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:30:22: #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 11:30:23: #2 number of paired peaks: 3984 INFO @ Thu, 30 Apr 2015 11:30:23: start model_add_line... INFO @ Thu, 30 Apr 2015 11:30:23: #1 tags after filtering in treatment: 4719423 INFO @ Thu, 30 Apr 2015 11:30:23: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:30:23: #1 finished! INFO @ Thu, 30 Apr 2015 11:30:23: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:30:24: #2 number of paired peaks: 3984 INFO @ Thu, 30 Apr 2015 11:30:24: start model_add_line... INFO @ Thu, 30 Apr 2015 11:30:38: start X-correlation... INFO @ Thu, 30 Apr 2015 11:30:38: end of X-cor INFO @ Thu, 30 Apr 2015 11:30:38: #2 finished! INFO @ Thu, 30 Apr 2015 11:30:38: #2 predicted fragment length is 156 bps INFO @ Thu, 30 Apr 2015 11:30:38: #2 alternative fragment length(s) may be 0,46,156,250,272 bps INFO @ Thu, 30 Apr 2015 11:30:38: #2.2 Generate R script for model : SRX113616.10_model.r INFO @ Thu, 30 Apr 2015 11:30:38: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:30:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:30:40: start X-correlation... INFO @ Thu, 30 Apr 2015 11:30:40: end of X-cor INFO @ Thu, 30 Apr 2015 11:30:40: #2 finished! INFO @ Thu, 30 Apr 2015 11:30:40: #2 predicted fragment length is 156 bps INFO @ Thu, 30 Apr 2015 11:30:40: #2 alternative fragment length(s) may be 0,46,156,250,272 bps INFO @ Thu, 30 Apr 2015 11:30:40: #2.2 Generate R script for model : SRX113616.05_model.r INFO @ Thu, 30 Apr 2015 11:30:40: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:30:40: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:30:40: start X-correlation... INFO @ Thu, 30 Apr 2015 11:30:40: end of X-cor INFO @ Thu, 30 Apr 2015 11:30:40: #2 finished! INFO @ Thu, 30 Apr 2015 11:30:40: #2 predicted fragment length is 156 bps INFO @ Thu, 30 Apr 2015 11:30:40: #2 alternative fragment length(s) may be 0,46,156,250,272 bps INFO @ Thu, 30 Apr 2015 11:30:40: #2.2 Generate R script for model : SRX113616.20_model.r INFO @ Thu, 30 Apr 2015 11:30:40: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:30:40: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:31:06: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:31:07: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:31:07: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:31:25: #4 Write output xls file... SRX113616.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:31:25: #4 Write peak in narrowPeak format file... SRX113616.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:31:25: #4 Write summits bed file... SRX113616.10_summits.bed INFO @ Thu, 30 Apr 2015 11:31:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (240 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:31:25: #4 Write output xls file... SRX113616.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:31:25: #4 Write peak in narrowPeak format file... SRX113616.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:31:25: #4 Write summits bed file... SRX113616.20_summits.bed INFO @ Thu, 30 Apr 2015 11:31:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (74 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:31:26: #4 Write output xls file... SRX113616.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:31:26: #4 Write peak in narrowPeak format file... SRX113616.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:31:26: #4 Write summits bed file... SRX113616.05_summits.bed INFO @ Thu, 30 Apr 2015 11:31:26: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (652 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。