Job ID = 3001480 sra ファイルのダウンロード中... Completed: 281088K bytes transferred in 10 seconds (211817K 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 2540 0 2540 0 0 4575 0 --:--:-- --:--:-- --:--:-- 6978 100 14953 0 14953 0 0 8568 0 --:--:-- 0:00:01 --:--:-- 9616 100 14953 0 14953 0 0 5444 0 --:--:-- 0:00:02 --:--:-- 5850 100 14953 0 14953 0 0 3990 0 --:--:-- 0:00:03 --:--:-- 4203 100 14953 0 14953 0 0 3148 0 --:--:-- 0:00:04 --:--:-- 3279 100 14953 0 14953 0 0 2599 0 --:--:-- 0:00:05 --:--:-- 2388 100 14953 0 14953 0 0 2214 0 --:--:-- 0:00:06 --:--:-- 0 100 17867 0 17867 0 0 2334 0 --:--:-- 0:00:07 --:--:-- 593 100 40377 0 40377 0 0 5108 0 --:--:-- 0:00:07 --:--:-- 6118 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 1124137 spots for /home/okishinya/chipatlas/results/ce10/SRX003823/SRR015063.sra Written 1124137 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: 00:00:08 1124137 reads; of these: 1124137 (100.00%) were unpaired; of these: 690805 (61.45%) aligned 0 times 369734 (32.89%) aligned exactly 1 time 63598 (5.66%) aligned >1 times 38.55% overall alignment rate Time searching: 00:00:08 Overall time: 00:00:08 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] 12698 / 433332 = 0.0293 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 18:44:41: # Command line: callpeak -t SRX003823.bam -f BAM -g ce -n SRX003823.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX003823.05 # format = BAM # ChIP-seq file = ['SRX003823.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 18:44:41: # Command line: callpeak -t SRX003823.bam -f BAM -g ce -n SRX003823.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX003823.20 # format = BAM # ChIP-seq file = ['SRX003823.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 18:44:41: # Command line: callpeak -t SRX003823.bam -f BAM -g ce -n SRX003823.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX003823.10 # format = BAM # ChIP-seq file = ['SRX003823.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 18:44:41: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:44:41: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:44:41: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:44:41: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:44:41: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:44:41: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:44:44: #1 tag size is determined as 36 bps INFO @ Mon, 07 Sep 2015 18:44:44: #1 tag size is determined as 36 bps INFO @ Mon, 07 Sep 2015 18:44:44: #1 tag size = 36 INFO @ Mon, 07 Sep 2015 18:44:44: #1 tag size = 36 INFO @ Mon, 07 Sep 2015 18:44:44: #1 total tags in treatment: 420634 INFO @ Mon, 07 Sep 2015 18:44:44: #1 total tags in treatment: 420634 INFO @ Mon, 07 Sep 2015 18:44:44: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:44:44: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:44:44: #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 18:44:44: #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 18:44:44: #1 tag size is determined as 36 bps INFO @ Mon, 07 Sep 2015 18:44:44: #1 tag size = 36 INFO @ Mon, 07 Sep 2015 18:44:44: #1 total tags in treatment: 420634 INFO @ Mon, 07 Sep 2015 18:44:44: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:44:44: #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 18:44:44: #1 tags after filtering in treatment: 420627 INFO @ Mon, 07 Sep 2015 18:44:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:44:44: #1 finished! INFO @ Mon, 07 Sep 2015 18:44:44: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:44:44: #1 tags after filtering in treatment: 420627 INFO @ Mon, 07 Sep 2015 18:44:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:44:44: #1 finished! INFO @ Mon, 07 Sep 2015 18:44:44: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:44:44: #1 tags after filtering in treatment: 420627 INFO @ Mon, 07 Sep 2015 18:44:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:44:44: #1 finished! INFO @ Mon, 07 Sep 2015 18:44:44: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:44:44: #2 number of paired peaks: 2698 INFO @ Mon, 07 Sep 2015 18:44:44: start model_add_line... INFO @ Mon, 07 Sep 2015 18:44:44: #2 number of paired peaks: 2698 INFO @ Mon, 07 Sep 2015 18:44:44: start model_add_line... INFO @ Mon, 07 Sep 2015 18:44:44: #2 number of paired peaks: 2698 INFO @ Mon, 07 Sep 2015 18:44:44: start model_add_line... INFO @ Mon, 07 Sep 2015 18:44:46: start X-correlation... INFO @ Mon, 07 Sep 2015 18:44:46: start X-correlation... INFO @ Mon, 07 Sep 2015 18:44:46: start X-correlation... INFO @ Mon, 07 Sep 2015 18:44:46: end of X-cor INFO @ Mon, 07 Sep 2015 18:44:46: #2 finished! INFO @ Mon, 07 Sep 2015 18:44:46: end of X-cor INFO @ Mon, 07 Sep 2015 18:44:46: end of X-cor INFO @ Mon, 07 Sep 2015 18:44:46: #2 finished! INFO @ Mon, 07 Sep 2015 18:44:46: #2 finished! INFO @ Mon, 07 Sep 2015 18:44:46: #2 predicted fragment length is 89 bps INFO @ Mon, 07 Sep 2015 18:44:46: #2 predicted fragment length is 89 bps INFO @ Mon, 07 Sep 2015 18:44:46: #2 predicted fragment length is 89 bps INFO @ Mon, 07 Sep 2015 18:44:46: #2 alternative fragment length(s) may be 89 bps INFO @ Mon, 07 Sep 2015 18:44:46: #2 alternative fragment length(s) may be 89 bps INFO @ Mon, 07 Sep 2015 18:44:46: #2 alternative fragment length(s) may be 89 bps INFO @ Mon, 07 Sep 2015 18:44:46: #2.2 Generate R script for model : SRX003823.10_model.r INFO @ Mon, 07 Sep 2015 18:44:46: #2.2 Generate R script for model : SRX003823.20_model.r INFO @ Mon, 07 Sep 2015 18:44:46: #2.2 Generate R script for model : SRX003823.05_model.r INFO @ Mon, 07 Sep 2015 18:44:46: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:44:46: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:44:46: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:44:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:44:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:44:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:44:49: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:44:49: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:44:49: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:44:50: #4 Write output xls file... SRX003823.20_peaks.xls INFO @ Mon, 07 Sep 2015 18:44:50: #4 Write peak in narrowPeak format file... SRX003823.20_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:44:50: #4 Write summits bed file... SRX003823.20_summits.bed INFO @ Mon, 07 Sep 2015 18:44:50: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (69 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:44:51: #4 Write output xls file... SRX003823.10_peaks.xls INFO @ Mon, 07 Sep 2015 18:44:51: #4 Write peak in narrowPeak format file... SRX003823.10_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:44:51: #4 Write summits bed file... SRX003823.10_summits.bed INFO @ Mon, 07 Sep 2015 18:44:51: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (282 records, 4 fields): 1 millis BedGraph に変換しました。 CompletedMACS2peakCalling BigWig に変換中... INFO @ Mon, 07 Sep 2015 18:44:51: #4 Write output xls file... SRX003823.05_peaks.xls INFO @ Mon, 07 Sep 2015 18:44:51: #4 Write peak in narrowPeak format file... SRX003823.05_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:44:51: #4 Write summits bed file... SRX003823.05_summits.bed INFO @ Mon, 07 Sep 2015 18:44:51: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (758 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。