Job ID = 3001504 sra ファイルのダウンロード中... Completed: 35521K bytes transferred in 3 seconds (75485K 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 --:--:-- --:--:-- --:--:-- 0 101 5467 0 5467 0 0 8852 0 --:--:-- --:--:-- --:--:-- 12803 100 14953 0 14953 0 0 8271 0 --:--:-- 0:00:01 --:--:-- 9247 100 14953 0 14953 0 0 5322 0 --:--:-- 0:00:02 --:--:-- 5709 100 14953 0 14953 0 0 3923 0 --:--:-- 0:00:03 --:--:-- 4130 100 14953 0 14953 0 0 3107 0 --:--:-- 0:00:04 --:--:-- 3235 100 14953 0 14953 0 0 2572 0 --:--:-- 0:00:05 --:--:-- 1825 100 14953 0 14953 0 0 2193 0 --:--:-- 0:00:06 --:--:-- 0 100 28781 0 28781 0 0 3769 0 --:--:-- 0:00:07 --:--:-- 2864 100 34434 0 34434 0 0 4400 0 --:--:-- 0:00:07 --:--:-- 4853 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 2045900 spots for /home/okishinya/chipatlas/results/ce10/SRX005638/SRR017607.sra Written 2045900 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: 00:00:18 2045900 reads; of these: 2045900 (100.00%) were unpaired; of these: 930760 (45.49%) aligned 0 times 856112 (41.85%) aligned exactly 1 time 259028 (12.66%) aligned >1 times 54.51% overall alignment rate Time searching: 00:00:18 Overall time: 00:00:18 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] 149280 / 1115140 = 0.1339 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 @ Mon, 07 Sep 2015 18:45:31: # Command line: callpeak -t SRX005638.bam -f BAM -g ce -n SRX005638.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX005638.20 # format = BAM # ChIP-seq file = ['SRX005638.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 @ Mon, 07 Sep 2015 18:45:31: # Command line: callpeak -t SRX005638.bam -f BAM -g ce -n SRX005638.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX005638.10 # format = BAM # ChIP-seq file = ['SRX005638.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 @ Mon, 07 Sep 2015 18:45:31: # Command line: callpeak -t SRX005638.bam -f BAM -g ce -n SRX005638.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX005638.05 # format = BAM # ChIP-seq file = ['SRX005638.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 @ Mon, 07 Sep 2015 18:45:31: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:45:31: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:45:31: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:45:31: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:45:31: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:45:31: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:45:36: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:45:36: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:45:36: #1 total tags in treatment: 965860 INFO @ Mon, 07 Sep 2015 18:45:36: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:45:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 Sep 2015 18:45:36: #1 tags after filtering in treatment: 965857 INFO @ Mon, 07 Sep 2015 18:45:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:45:36: #1 finished! INFO @ Mon, 07 Sep 2015 18:45:36: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:45:36: #2 number of paired peaks: 374 WARNING @ Mon, 07 Sep 2015 18:45:36: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Mon, 07 Sep 2015 18:45:36: start model_add_line... INFO @ Mon, 07 Sep 2015 18:45:36: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:45:36: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:45:36: #1 total tags in treatment: 965860 INFO @ Mon, 07 Sep 2015 18:45:36: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:45:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 Sep 2015 18:45:37: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:45:37: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:45:37: #1 total tags in treatment: 965860 INFO @ Mon, 07 Sep 2015 18:45:37: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:45:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 Sep 2015 18:45:37: #1 tags after filtering in treatment: 965857 INFO @ Mon, 07 Sep 2015 18:45:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:45:37: #1 finished! INFO @ Mon, 07 Sep 2015 18:45:37: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:45:37: #1 tags after filtering in treatment: 965857 INFO @ Mon, 07 Sep 2015 18:45:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:45:37: #1 finished! INFO @ Mon, 07 Sep 2015 18:45:37: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:45:37: start X-correlation... INFO @ Mon, 07 Sep 2015 18:45:37: #2 number of paired peaks: 374 WARNING @ Mon, 07 Sep 2015 18:45:37: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Mon, 07 Sep 2015 18:45:37: start model_add_line... INFO @ Mon, 07 Sep 2015 18:45:37: end of X-cor INFO @ Mon, 07 Sep 2015 18:45:37: #2 finished! INFO @ Mon, 07 Sep 2015 18:45:37: #2 predicted fragment length is 100 bps INFO @ Mon, 07 Sep 2015 18:45:37: #2 alternative fragment length(s) may be 56,100,583 bps INFO @ Mon, 07 Sep 2015 18:45:37: #2.2 Generate R script for model : SRX005638.20_model.r INFO @ Mon, 07 Sep 2015 18:45:37: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:45:37: #2 number of paired peaks: 374 WARNING @ Mon, 07 Sep 2015 18:45:37: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Mon, 07 Sep 2015 18:45:37: start model_add_line... INFO @ Mon, 07 Sep 2015 18:45:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:45:38: start X-correlation... INFO @ Mon, 07 Sep 2015 18:45:38: start X-correlation... INFO @ Mon, 07 Sep 2015 18:45:38: end of X-cor INFO @ Mon, 07 Sep 2015 18:45:38: #2 finished! INFO @ Mon, 07 Sep 2015 18:45:38: #2 predicted fragment length is 100 bps INFO @ Mon, 07 Sep 2015 18:45:38: #2 alternative fragment length(s) may be 56,100,583 bps INFO @ Mon, 07 Sep 2015 18:45:38: #2.2 Generate R script for model : SRX005638.05_model.r INFO @ Mon, 07 Sep 2015 18:45:38: end of X-cor INFO @ Mon, 07 Sep 2015 18:45:38: #2 finished! INFO @ Mon, 07 Sep 2015 18:45:38: #2 predicted fragment length is 100 bps INFO @ Mon, 07 Sep 2015 18:45:38: #2 alternative fragment length(s) may be 56,100,583 bps INFO @ Mon, 07 Sep 2015 18:45:38: #2.2 Generate R script for model : SRX005638.10_model.r INFO @ Mon, 07 Sep 2015 18:45:38: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:45:38: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:45:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:45:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:45:43: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:45:44: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:45:44: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:45:47: #4 Write output xls file... SRX005638.20_peaks.xls INFO @ Mon, 07 Sep 2015 18:45:47: #4 Write peak in narrowPeak format file... SRX005638.20_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:45:47: #4 Write summits bed file... SRX005638.20_summits.bed INFO @ Mon, 07 Sep 2015 18:45:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (32 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:45:48: #4 Write output xls file... SRX005638.05_peaks.xls INFO @ Mon, 07 Sep 2015 18:45:48: #4 Write peak in narrowPeak format file... SRX005638.05_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:45:48: #4 Write summits bed file... SRX005638.05_summits.bed INFO @ Mon, 07 Sep 2015 18:45:48: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (204 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:45:48: #4 Write output xls file... SRX005638.10_peaks.xls INFO @ Mon, 07 Sep 2015 18:45:48: #4 Write peak in narrowPeak format file... SRX005638.10_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:45:48: #4 Write summits bed file... SRX005638.10_summits.bed INFO @ Mon, 07 Sep 2015 18:45:48: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (87 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。