Job ID = 2236698 sra ファイルのダウンロード中... Completed: 301645K bytes transferred in 5 seconds (428969K 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 35020 0 35020 0 0 43812 0 --:--:-- --:--:-- --:--:-- 57598 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 16264926 spots for /home/okishinya/chipatlas/results/ce10/SRX027211/SRR066594.sra Written 16264926 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: 00:01:46 16264926 reads; of these: 16264926 (100.00%) were unpaired; of these: 10753195 (66.11%) aligned 0 times 4783177 (29.41%) aligned exactly 1 time 728554 (4.48%) aligned >1 times 33.89% overall alignment rate Time searching: 00:01:46 Overall time: 00:01:46 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] 660413 / 5511731 = 0.1198 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 10:59:04: # Command line: callpeak -t SRX027211.bam -f BAM -g ce -n SRX027211.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX027211.10 # format = BAM # ChIP-seq file = ['SRX027211.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 10:59:04: #1 read tag files... INFO @ Thu, 30 Apr 2015 10:59:04: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 10:59:04: # Command line: callpeak -t SRX027211.bam -f BAM -g ce -n SRX027211.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX027211.20 # format = BAM # ChIP-seq file = ['SRX027211.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 10:59:04: #1 read tag files... INFO @ Thu, 30 Apr 2015 10:59:04: # Command line: callpeak -t SRX027211.bam -f BAM -g ce -n SRX027211.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX027211.05 # format = BAM # ChIP-seq file = ['SRX027211.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 10:59:04: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 10:59:04: #1 read tag files... INFO @ Thu, 30 Apr 2015 10:59:04: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 10:59:11: 1000000 INFO @ Thu, 30 Apr 2015 10:59:11: 1000000 INFO @ Thu, 30 Apr 2015 10:59:11: 1000000 INFO @ Thu, 30 Apr 2015 10:59:17: 2000000 INFO @ Thu, 30 Apr 2015 10:59:17: 2000000 INFO @ Thu, 30 Apr 2015 10:59:17: 2000000 INFO @ Thu, 30 Apr 2015 10:59:24: 3000000 INFO @ Thu, 30 Apr 2015 10:59:24: 3000000 INFO @ Thu, 30 Apr 2015 10:59:24: 3000000 INFO @ Thu, 30 Apr 2015 10:59:30: 4000000 INFO @ Thu, 30 Apr 2015 10:59:30: 4000000 INFO @ Thu, 30 Apr 2015 10:59:30: 4000000 INFO @ Thu, 30 Apr 2015 10:59:36: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 10:59:36: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 10:59:36: #1 total tags in treatment: 4851318 INFO @ Thu, 30 Apr 2015 10:59:36: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 10:59:36: #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 10:59:36: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 10:59:36: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 10:59:36: #1 total tags in treatment: 4851318 INFO @ Thu, 30 Apr 2015 10:59:36: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 10:59:36: #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 10:59:36: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 10:59:36: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 10:59:36: #1 total tags in treatment: 4851318 INFO @ Thu, 30 Apr 2015 10:59:36: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 10:59:36: #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 10:59:36: #1 tags after filtering in treatment: 4851053 INFO @ Thu, 30 Apr 2015 10:59:36: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 10:59:36: #1 finished! INFO @ Thu, 30 Apr 2015 10:59:36: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 10:59:36: #1 tags after filtering in treatment: 4851053 INFO @ Thu, 30 Apr 2015 10:59:36: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 10:59:36: #1 finished! INFO @ Thu, 30 Apr 2015 10:59:36: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 10:59:36: #1 tags after filtering in treatment: 4851053 INFO @ Thu, 30 Apr 2015 10:59:36: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 10:59:36: #1 finished! INFO @ Thu, 30 Apr 2015 10:59:36: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 10:59:38: #2 number of paired peaks: 2977 INFO @ Thu, 30 Apr 2015 10:59:38: start model_add_line... INFO @ Thu, 30 Apr 2015 10:59:38: #2 number of paired peaks: 2977 INFO @ Thu, 30 Apr 2015 10:59:38: start model_add_line... INFO @ Thu, 30 Apr 2015 10:59:38: #2 number of paired peaks: 2977 INFO @ Thu, 30 Apr 2015 10:59:38: start model_add_line... INFO @ Thu, 30 Apr 2015 10:59:51: start X-correlation... INFO @ Thu, 30 Apr 2015 10:59:51: end of X-cor INFO @ Thu, 30 Apr 2015 10:59:51: #2 finished! INFO @ Thu, 30 Apr 2015 10:59:51: #2 predicted fragment length is 243 bps INFO @ Thu, 30 Apr 2015 10:59:51: #2 alternative fragment length(s) may be 243 bps INFO @ Thu, 30 Apr 2015 10:59:51: #2.2 Generate R script for model : SRX027211.10_model.r INFO @ Thu, 30 Apr 2015 10:59:51: #3 Call peaks... INFO @ Thu, 30 Apr 2015 10:59:51: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 10:59:51: start X-correlation... INFO @ Thu, 30 Apr 2015 10:59:51: end of X-cor INFO @ Thu, 30 Apr 2015 10:59:51: #2 finished! INFO @ Thu, 30 Apr 2015 10:59:51: #2 predicted fragment length is 243 bps INFO @ Thu, 30 Apr 2015 10:59:51: #2 alternative fragment length(s) may be 243 bps INFO @ Thu, 30 Apr 2015 10:59:51: #2.2 Generate R script for model : SRX027211.20_model.r INFO @ Thu, 30 Apr 2015 10:59:51: #3 Call peaks... INFO @ Thu, 30 Apr 2015 10:59:51: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 10:59:51: start X-correlation... INFO @ Thu, 30 Apr 2015 10:59:51: end of X-cor INFO @ Thu, 30 Apr 2015 10:59:51: #2 finished! INFO @ Thu, 30 Apr 2015 10:59:51: #2 predicted fragment length is 243 bps INFO @ Thu, 30 Apr 2015 10:59:51: #2 alternative fragment length(s) may be 243 bps INFO @ Thu, 30 Apr 2015 10:59:51: #2.2 Generate R script for model : SRX027211.05_model.r INFO @ Thu, 30 Apr 2015 10:59:51: #3 Call peaks... INFO @ Thu, 30 Apr 2015 10:59:51: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:00:21: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:00:22: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:00:22: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:00:44: #4 Write output xls file... SRX027211.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:00:44: #4 Write peak in narrowPeak format file... SRX027211.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:00:44: #4 Write summits bed file... SRX027211.20_summits.bed INFO @ Thu, 30 Apr 2015 11:00:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2161 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:00:47: #4 Write output xls file... SRX027211.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:00:47: #4 Write peak in narrowPeak format file... SRX027211.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:00:47: #4 Write summits bed file... SRX027211.10_summits.bed INFO @ Thu, 30 Apr 2015 11:00:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3107 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:00:49: #4 Write output xls file... SRX027211.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:00:49: #4 Write peak in narrowPeak format file... SRX027211.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:00:49: #4 Write summits bed file... SRX027211.05_summits.bed INFO @ Thu, 30 Apr 2015 11:00:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3892 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。