Job ID = 2236885 sra ファイルのダウンロード中... Completed: 149567K bytes transferred in 13 seconds (88678K 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 35137 0 35137 0 0 46105 0 --:--:-- --:--:-- --:--:-- 61643 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 8845185 spots for /home/okishinya/chipatlas/results/ce10/SRX059267/SRR190707.sra Written 8845185 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: 00:00:38 8845185 reads; of these: 8845185 (100.00%) were unpaired; of these: 7707092 (87.13%) aligned 0 times 925589 (10.46%) aligned exactly 1 time 212504 (2.40%) aligned >1 times 12.87% overall alignment rate Time searching: 00:00:38 Overall time: 00:00:38 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] 172295 / 1138093 = 0.1514 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 11:12:15: # Command line: callpeak -t SRX059267.bam -f BAM -g ce -n SRX059267.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX059267.05 # format = BAM # ChIP-seq file = ['SRX059267.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 11:12:15: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:12:15: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:12:15: # Command line: callpeak -t SRX059267.bam -f BAM -g ce -n SRX059267.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX059267.10 # format = BAM # ChIP-seq file = ['SRX059267.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 11:12:15: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:12:15: # Command line: callpeak -t SRX059267.bam -f BAM -g ce -n SRX059267.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX059267.20 # format = BAM # ChIP-seq file = ['SRX059267.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 11:12:15: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:12:15: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:12:15: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:12:20: #1 tag size is determined as 28 bps INFO @ Thu, 30 Apr 2015 11:12:20: #1 tag size = 28 INFO @ Thu, 30 Apr 2015 11:12:20: #1 total tags in treatment: 965798 INFO @ Thu, 30 Apr 2015 11:12:20: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:12:20: #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 11:12:20: #1 tag size is determined as 28 bps INFO @ Thu, 30 Apr 2015 11:12:20: #1 tag size = 28 INFO @ Thu, 30 Apr 2015 11:12:20: #1 total tags in treatment: 965798 INFO @ Thu, 30 Apr 2015 11:12:20: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:12:20: #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 11:12:20: #1 tags after filtering in treatment: 965790 INFO @ Thu, 30 Apr 2015 11:12:20: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:12:20: #1 finished! INFO @ Thu, 30 Apr 2015 11:12:20: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:12:20: #1 tags after filtering in treatment: 965790 INFO @ Thu, 30 Apr 2015 11:12:20: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:12:20: #1 finished! INFO @ Thu, 30 Apr 2015 11:12:20: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:12:20: #1 tag size is determined as 28 bps INFO @ Thu, 30 Apr 2015 11:12:20: #1 tag size = 28 INFO @ Thu, 30 Apr 2015 11:12:20: #1 total tags in treatment: 965798 INFO @ Thu, 30 Apr 2015 11:12:20: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:12:20: #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 11:12:21: #1 tags after filtering in treatment: 965790 INFO @ Thu, 30 Apr 2015 11:12:21: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:12:21: #1 finished! INFO @ Thu, 30 Apr 2015 11:12:21: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:12:21: #2 number of paired peaks: 1203 INFO @ Thu, 30 Apr 2015 11:12:21: start model_add_line... INFO @ Thu, 30 Apr 2015 11:12:21: #2 number of paired peaks: 1203 INFO @ Thu, 30 Apr 2015 11:12:21: start model_add_line... INFO @ Thu, 30 Apr 2015 11:12:21: #2 number of paired peaks: 1203 INFO @ Thu, 30 Apr 2015 11:12:21: start model_add_line... INFO @ Thu, 30 Apr 2015 11:12:22: start X-correlation... INFO @ Thu, 30 Apr 2015 11:12:22: end of X-cor INFO @ Thu, 30 Apr 2015 11:12:22: #2 finished! INFO @ Thu, 30 Apr 2015 11:12:22: #2 predicted fragment length is 167 bps INFO @ Thu, 30 Apr 2015 11:12:22: #2 alternative fragment length(s) may be 167 bps INFO @ Thu, 30 Apr 2015 11:12:22: #2.2 Generate R script for model : SRX059267.10_model.r INFO @ Thu, 30 Apr 2015 11:12:22: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:12:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:12:22: start X-correlation... INFO @ Thu, 30 Apr 2015 11:12:22: end of X-cor INFO @ Thu, 30 Apr 2015 11:12:22: #2 finished! INFO @ Thu, 30 Apr 2015 11:12:22: #2 predicted fragment length is 167 bps INFO @ Thu, 30 Apr 2015 11:12:22: #2 alternative fragment length(s) may be 167 bps INFO @ Thu, 30 Apr 2015 11:12:22: #2.2 Generate R script for model : SRX059267.05_model.r INFO @ Thu, 30 Apr 2015 11:12:22: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:12:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:12:22: start X-correlation... INFO @ Thu, 30 Apr 2015 11:12:23: end of X-cor INFO @ Thu, 30 Apr 2015 11:12:23: #2 finished! INFO @ Thu, 30 Apr 2015 11:12:23: #2 predicted fragment length is 167 bps INFO @ Thu, 30 Apr 2015 11:12:23: #2 alternative fragment length(s) may be 167 bps INFO @ Thu, 30 Apr 2015 11:12:23: #2.2 Generate R script for model : SRX059267.20_model.r INFO @ Thu, 30 Apr 2015 11:12:23: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:12:23: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:12:28: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:12:28: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:12:29: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 30 Apr 2015 11:12:33: #4 Write output xls file... SRX059267.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:12:33: #4 Write output xls file... SRX059267.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:12:33: #4 Write peak in narrowPeak format file... SRX059267.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:12:33: #4 Write peak in narrowPeak format file... SRX059267.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:12:33: #4 Write summits bed file... SRX059267.10_summits.bed INFO @ Thu, 30 Apr 2015 11:12:33: Done! INFO @ Thu, 30 Apr 2015 11:12:33: #4 Write summits bed file... SRX059267.05_summits.bed INFO @ Thu, 30 Apr 2015 11:12:33: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (567 records, 4 fields): 3 millis pass1 - making usageList (7 chroms): 1 millis CompletedMACS2peakCalling pass2 - checking and writing primary data (861 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:12:33: #4 Write output xls file... SRX059267.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:12:33: #4 Write peak in narrowPeak format file... SRX059267.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:12:33: #4 Write summits bed file... SRX059267.20_summits.bed INFO @ Thu, 30 Apr 2015 11:12:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (328 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。