Job ID = 2237041 sra ファイルのダウンロード中... Completed: 79676K bytes transferred in 5 seconds (127708K 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 37990 0 37990 0 0 51407 0 --:--:-- --:--:-- --:--:-- 69451 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 4663656 spots for /home/okishinya/chipatlas/results/ce10/SRX080096/SRR298916.sra Written 4663656 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: 00:00:27 4663656 reads; of these: 4663656 (100.00%) were unpaired; of these: 3310568 (70.99%) aligned 0 times 1138560 (24.41%) aligned exactly 1 time 214528 (4.60%) aligned >1 times 29.01% overall alignment rate Time searching: 00:00:27 Overall time: 00:00:27 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] 261029 / 1353088 = 0.1929 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 11:25:13: # Command line: callpeak -t SRX080096.bam -f BAM -g ce -n SRX080096.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX080096.05 # format = BAM # ChIP-seq file = ['SRX080096.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 11:25:13: # Command line: callpeak -t SRX080096.bam -f BAM -g ce -n SRX080096.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX080096.10 # format = BAM # ChIP-seq file = ['SRX080096.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 11:25:13: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:25:13: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:25:13: # Command line: callpeak -t SRX080096.bam -f BAM -g ce -n SRX080096.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX080096.20 # format = BAM # ChIP-seq file = ['SRX080096.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 11:25:13: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:25:13: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:25:13: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:25:13: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:25:19: 1000000 INFO @ Thu, 30 Apr 2015 11:25:19: 1000000 INFO @ Thu, 30 Apr 2015 11:25:19: 1000000 INFO @ Thu, 30 Apr 2015 11:25:19: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:25:19: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:25:19: #1 total tags in treatment: 1092059 INFO @ Thu, 30 Apr 2015 11:25:19: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:25:19: #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 11:25:19: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:25:19: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:25:19: #1 total tags in treatment: 1092059 INFO @ Thu, 30 Apr 2015 11:25:19: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:25:19: #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 11:25:19: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:25:19: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:25:19: #1 total tags in treatment: 1092059 INFO @ Thu, 30 Apr 2015 11:25:19: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:25:19: #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 11:25:19: #1 tags after filtering in treatment: 1092022 INFO @ Thu, 30 Apr 2015 11:25:19: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:25:19: #1 finished! INFO @ Thu, 30 Apr 2015 11:25:19: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:25:20: #1 tags after filtering in treatment: 1092022 INFO @ Thu, 30 Apr 2015 11:25:20: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:25:20: #1 finished! INFO @ Thu, 30 Apr 2015 11:25:20: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:25:20: #1 tags after filtering in treatment: 1092022 INFO @ Thu, 30 Apr 2015 11:25:20: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:25:20: #1 finished! INFO @ Thu, 30 Apr 2015 11:25:20: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:25:20: #2 number of paired peaks: 1588 INFO @ Thu, 30 Apr 2015 11:25:20: start model_add_line... INFO @ Thu, 30 Apr 2015 11:25:20: #2 number of paired peaks: 1588 INFO @ Thu, 30 Apr 2015 11:25:20: start model_add_line... INFO @ Thu, 30 Apr 2015 11:25:20: #2 number of paired peaks: 1588 INFO @ Thu, 30 Apr 2015 11:25:20: start model_add_line... INFO @ Thu, 30 Apr 2015 11:25:22: start X-correlation... INFO @ Thu, 30 Apr 2015 11:25:22: end of X-cor INFO @ Thu, 30 Apr 2015 11:25:22: #2 finished! INFO @ Thu, 30 Apr 2015 11:25:22: #2 predicted fragment length is 125 bps INFO @ Thu, 30 Apr 2015 11:25:22: #2 alternative fragment length(s) may be 125 bps INFO @ Thu, 30 Apr 2015 11:25:22: #2.2 Generate R script for model : SRX080096.20_model.r INFO @ Thu, 30 Apr 2015 11:25:22: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:25:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:25:22: start X-correlation... INFO @ Thu, 30 Apr 2015 11:25:22: end of X-cor INFO @ Thu, 30 Apr 2015 11:25:22: #2 finished! INFO @ Thu, 30 Apr 2015 11:25:22: #2 predicted fragment length is 125 bps INFO @ Thu, 30 Apr 2015 11:25:22: #2 alternative fragment length(s) may be 125 bps INFO @ Thu, 30 Apr 2015 11:25:22: #2.2 Generate R script for model : SRX080096.10_model.r INFO @ Thu, 30 Apr 2015 11:25:22: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:25:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:25:22: start X-correlation... INFO @ Thu, 30 Apr 2015 11:25:22: end of X-cor INFO @ Thu, 30 Apr 2015 11:25:22: #2 finished! INFO @ Thu, 30 Apr 2015 11:25:22: #2 predicted fragment length is 125 bps INFO @ Thu, 30 Apr 2015 11:25:22: #2 alternative fragment length(s) may be 125 bps INFO @ Thu, 30 Apr 2015 11:25:22: #2.2 Generate R script for model : SRX080096.05_model.r INFO @ Thu, 30 Apr 2015 11:25:22: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:25:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:25:29: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:25:29: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:25:29: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:25:34: #4 Write output xls file... SRX080096.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:25:34: #4 Write peak in narrowPeak format file... SRX080096.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:25:34: #4 Write summits bed file... SRX080096.20_summits.bed INFO @ Thu, 30 Apr 2015 11:25:34: Done! INFO @ Thu, 30 Apr 2015 11:25:34: #4 Write output xls file... SRX080096.10_peaks.xls pass1 - making usageList (6 chroms): 1 millis INFO @ Thu, 30 Apr 2015 11:25:34: #4 Write peak in narrowPeak format file... SRX080096.10_peaks.narrowPeak pass2 - checking and writing primary data (694 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:25:34: #4 Write summits bed file... SRX080096.10_summits.bed INFO @ Thu, 30 Apr 2015 11:25:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1118 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:25:35: #4 Write output xls file... SRX080096.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:25:35: #4 Write peak in narrowPeak format file... SRX080096.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:25:35: #4 Write summits bed file... SRX080096.05_summits.bed INFO @ Thu, 30 Apr 2015 11:25:35: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1694 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。