Job ID = 2237037 sra ファイルのダウンロード中... Completed: 56834K bytes transferred in 4 seconds (108162K 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 9839 0 9839 0 0 20048 0 --:--:-- --:--:-- --:--:-- 32796 100 38019 0 38019 0 0 55850 0 --:--:-- --:--:-- --:--:-- 77589 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 2955703 spots for /home/okishinya/chipatlas/results/ce10/SRX080092/SRR298912.sra Written 2955703 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: 00:00:22 2955703 reads; of these: 2955703 (100.00%) were unpaired; of these: 1645911 (55.69%) aligned 0 times 1104850 (37.38%) aligned exactly 1 time 204942 (6.93%) aligned >1 times 44.31% overall alignment rate Time searching: 00:00:22 Overall time: 00:00:22 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] 178121 / 1309792 = 0.1360 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 11:25:02: # Command line: callpeak -t SRX080092.bam -f BAM -g ce -n SRX080092.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX080092.05 # format = BAM # ChIP-seq file = ['SRX080092.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 11:25:02: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:25:02: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:25:02: # Command line: callpeak -t SRX080092.bam -f BAM -g ce -n SRX080092.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX080092.20 # format = BAM # ChIP-seq file = ['SRX080092.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 11:25:02: # Command line: callpeak -t SRX080092.bam -f BAM -g ce -n SRX080092.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX080092.10 # format = BAM # ChIP-seq file = ['SRX080092.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 11:25:02: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:25:02: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:25:02: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:25:02: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:25:06: 1000000 INFO @ Thu, 30 Apr 2015 11:25:07: 1000000 INFO @ Thu, 30 Apr 2015 11:25:07: 1000000 INFO @ Thu, 30 Apr 2015 11:25:07: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:25:07: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:25:07: #1 total tags in treatment: 1131671 INFO @ Thu, 30 Apr 2015 11:25:07: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:25:07: #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 11:25:07: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:25:07: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:25:07: #1 total tags in treatment: 1131671 INFO @ Thu, 30 Apr 2015 11:25:07: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:25:07: #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 11:25:07: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:25:07: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:25:07: #1 total tags in treatment: 1131671 INFO @ Thu, 30 Apr 2015 11:25:07: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:25:07: #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 11:25:07: #1 tags after filtering in treatment: 1131645 INFO @ Thu, 30 Apr 2015 11:25:07: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:25:07: #1 finished! INFO @ Thu, 30 Apr 2015 11:25:07: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:25:07: #1 tags after filtering in treatment: 1131645 INFO @ Thu, 30 Apr 2015 11:25:07: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:25:07: #1 finished! INFO @ Thu, 30 Apr 2015 11:25:07: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:25:07: #1 tags after filtering in treatment: 1131645 INFO @ Thu, 30 Apr 2015 11:25:07: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:25:07: #1 finished! INFO @ Thu, 30 Apr 2015 11:25:07: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:25:08: #2 number of paired peaks: 1108 INFO @ Thu, 30 Apr 2015 11:25:08: start model_add_line... INFO @ Thu, 30 Apr 2015 11:25:08: #2 number of paired peaks: 1108 INFO @ Thu, 30 Apr 2015 11:25:08: start model_add_line... INFO @ Thu, 30 Apr 2015 11:25:08: #2 number of paired peaks: 1108 INFO @ Thu, 30 Apr 2015 11:25:08: start model_add_line... INFO @ Thu, 30 Apr 2015 11:25:09: start X-correlation... INFO @ Thu, 30 Apr 2015 11:25:09: end of X-cor INFO @ Thu, 30 Apr 2015 11:25:09: #2 finished! INFO @ Thu, 30 Apr 2015 11:25:09: #2 predicted fragment length is 145 bps INFO @ Thu, 30 Apr 2015 11:25:09: #2 alternative fragment length(s) may be 145 bps INFO @ Thu, 30 Apr 2015 11:25:09: #2.2 Generate R script for model : SRX080092.20_model.r INFO @ Thu, 30 Apr 2015 11:25:09: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:25:09: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:25:09: start X-correlation... INFO @ Thu, 30 Apr 2015 11:25:09: end of X-cor INFO @ Thu, 30 Apr 2015 11:25:09: #2 finished! INFO @ Thu, 30 Apr 2015 11:25:09: #2 predicted fragment length is 145 bps INFO @ Thu, 30 Apr 2015 11:25:09: #2 alternative fragment length(s) may be 145 bps INFO @ Thu, 30 Apr 2015 11:25:09: #2.2 Generate R script for model : SRX080092.05_model.r INFO @ Thu, 30 Apr 2015 11:25:09: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:25:09: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:25:09: start X-correlation... INFO @ Thu, 30 Apr 2015 11:25:09: end of X-cor INFO @ Thu, 30 Apr 2015 11:25:09: #2 finished! INFO @ Thu, 30 Apr 2015 11:25:09: #2 predicted fragment length is 145 bps INFO @ Thu, 30 Apr 2015 11:25:09: #2 alternative fragment length(s) may be 145 bps INFO @ Thu, 30 Apr 2015 11:25:09: #2.2 Generate R script for model : SRX080092.10_model.r INFO @ Thu, 30 Apr 2015 11:25:09: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:25:09: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:25:16: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:25:16: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:25:16: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:25:21: #4 Write output xls file... SRX080092.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:25:21: #4 Write peak in narrowPeak format file... SRX080092.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:25:21: #4 Write summits bed file... SRX080092.20_summits.bed INFO @ Thu, 30 Apr 2015 11:25:21: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (457 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:25:22: #4 Write output xls file... SRX080092.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:25:22: #4 Write peak in narrowPeak format file... SRX080092.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:25:22: #4 Write summits bed file... SRX080092.10_summits.bed INFO @ Thu, 30 Apr 2015 11:25:22: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (753 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:25:22: #4 Write output xls file... SRX080092.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:25:22: #4 Write peak in narrowPeak format file... SRX080092.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:25:22: #4 Write summits bed file... SRX080092.05_summits.bed INFO @ Thu, 30 Apr 2015 11:25:22: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1169 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。