Job ID = 2161911 sra ファイルのダウンロード中... Completed: 632723K bytes transferred in 8 seconds (601782K 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 23665 0 23665 0 0 30765 0 --:--:-- --:--:-- --:--:-- 40942 100 36285 0 36285 0 0 47119 0 --:--:-- --:--:-- --:--:-- 62668 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 25688390 spots for /home/okishinya/chipatlas/results/dm3/SRX040615/SRR097984.sra Written 25688390 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: 00:05:00 25688390 reads; of these: 25688390 (100.00%) were unpaired; of these: 2336858 (9.10%) aligned 0 times 22329614 (86.92%) aligned exactly 1 time 1021918 (3.98%) aligned >1 times 90.90% overall alignment rate Time searching: 00:05:00 Overall time: 00:05:00 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 16042298 / 23351532 = 0.6870 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 @ Tue, 21 Apr 2015 13:20:59: # Command line: callpeak -t SRX040615.bam -f BAM -g dm -n SRX040615.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX040615.10 # format = BAM # ChIP-seq file = ['SRX040615.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 21 Apr 2015 13:20:59: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:20:59: # Command line: callpeak -t SRX040615.bam -f BAM -g dm -n SRX040615.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX040615.20 # format = BAM # ChIP-seq file = ['SRX040615.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 21 Apr 2015 13:20:59: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:20:59: # Command line: callpeak -t SRX040615.bam -f BAM -g dm -n SRX040615.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX040615.05 # format = BAM # ChIP-seq file = ['SRX040615.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 21 Apr 2015 13:20:59: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:20:59: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:20:59: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:20:59: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:21:04: 1000000 INFO @ Tue, 21 Apr 2015 13:21:04: 1000000 INFO @ Tue, 21 Apr 2015 13:21:04: 1000000 INFO @ Tue, 21 Apr 2015 13:21:09: 2000000 INFO @ Tue, 21 Apr 2015 13:21:09: 2000000 INFO @ Tue, 21 Apr 2015 13:21:09: 2000000 INFO @ Tue, 21 Apr 2015 13:21:14: 3000000 INFO @ Tue, 21 Apr 2015 13:21:14: 3000000 INFO @ Tue, 21 Apr 2015 13:21:14: 3000000 INFO @ Tue, 21 Apr 2015 13:21:18: 4000000 INFO @ Tue, 21 Apr 2015 13:21:18: 4000000 INFO @ Tue, 21 Apr 2015 13:21:19: 4000000 INFO @ Tue, 21 Apr 2015 13:21:23: 5000000 INFO @ Tue, 21 Apr 2015 13:21:23: 5000000 INFO @ Tue, 21 Apr 2015 13:21:24: 5000000 INFO @ Tue, 21 Apr 2015 13:21:28: 6000000 INFO @ Tue, 21 Apr 2015 13:21:28: 6000000 INFO @ Tue, 21 Apr 2015 13:21:30: 6000000 INFO @ Tue, 21 Apr 2015 13:21:33: 7000000 INFO @ Tue, 21 Apr 2015 13:21:33: 7000000 INFO @ Tue, 21 Apr 2015 13:21:34: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 13:21:34: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 13:21:34: #1 total tags in treatment: 7309234 INFO @ Tue, 21 Apr 2015 13:21:34: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:21:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 13:21:35: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 13:21:35: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 13:21:35: #1 total tags in treatment: 7309234 INFO @ Tue, 21 Apr 2015 13:21:35: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:21:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 13:21:35: 7000000 INFO @ Tue, 21 Apr 2015 13:21:36: #1 tags after filtering in treatment: 7304967 INFO @ Tue, 21 Apr 2015 13:21:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:21:36: #1 finished! INFO @ Tue, 21 Apr 2015 13:21:36: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:21:36: #1 tags after filtering in treatment: 7304967 INFO @ Tue, 21 Apr 2015 13:21:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:21:36: #1 finished! INFO @ Tue, 21 Apr 2015 13:21:36: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:21:36: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 13:21:36: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 13:21:36: #1 total tags in treatment: 7309234 INFO @ Tue, 21 Apr 2015 13:21:36: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:21:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 13:21:38: #1 tags after filtering in treatment: 7304967 INFO @ Tue, 21 Apr 2015 13:21:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:21:38: #1 finished! INFO @ Tue, 21 Apr 2015 13:21:38: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:21:38: #2 number of paired peaks: 11110 INFO @ Tue, 21 Apr 2015 13:21:38: start model_add_line... INFO @ Tue, 21 Apr 2015 13:21:39: #2 number of paired peaks: 11110 INFO @ Tue, 21 Apr 2015 13:21:39: start model_add_line... INFO @ Tue, 21 Apr 2015 13:21:40: #2 number of paired peaks: 11110 INFO @ Tue, 21 Apr 2015 13:21:40: start model_add_line... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 21 Apr 2015 13:23:13: start X-correlation... INFO @ Tue, 21 Apr 2015 13:23:13: end of X-cor INFO @ Tue, 21 Apr 2015 13:23:13: #2 finished! INFO @ Tue, 21 Apr 2015 13:23:13: #2 predicted fragment length is 171 bps INFO @ Tue, 21 Apr 2015 13:23:13: #2 alternative fragment length(s) may be 171 bps INFO @ Tue, 21 Apr 2015 13:23:13: #2.2 Generate R script for model : SRX040615.20_model.r INFO @ Tue, 21 Apr 2015 13:23:13: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:23:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:23:13: start X-correlation... INFO @ Tue, 21 Apr 2015 13:23:13: end of X-cor INFO @ Tue, 21 Apr 2015 13:23:13: #2 finished! INFO @ Tue, 21 Apr 2015 13:23:13: #2 predicted fragment length is 171 bps INFO @ Tue, 21 Apr 2015 13:23:13: #2 alternative fragment length(s) may be 171 bps INFO @ Tue, 21 Apr 2015 13:23:13: #2.2 Generate R script for model : SRX040615.05_model.r INFO @ Tue, 21 Apr 2015 13:23:13: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:23:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:23:15: start X-correlation... INFO @ Tue, 21 Apr 2015 13:23:15: end of X-cor INFO @ Tue, 21 Apr 2015 13:23:15: #2 finished! INFO @ Tue, 21 Apr 2015 13:23:15: #2 predicted fragment length is 171 bps INFO @ Tue, 21 Apr 2015 13:23:15: #2 alternative fragment length(s) may be 171 bps INFO @ Tue, 21 Apr 2015 13:23:15: #2.2 Generate R script for model : SRX040615.10_model.r INFO @ Tue, 21 Apr 2015 13:23:15: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:23:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:24:06: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:24:06: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:24:08: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:24:43: #4 Write output xls file... SRX040615.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:24:44: #4 Write peak in narrowPeak format file... SRX040615.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:24:44: #4 Write summits bed file... SRX040615.20_summits.bed INFO @ Tue, 21 Apr 2015 13:24:44: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7310 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:24:49: #4 Write output xls file... SRX040615.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:24:50: #4 Write peak in narrowPeak format file... SRX040615.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:24:50: #4 Write summits bed file... SRX040615.10_summits.bed INFO @ Tue, 21 Apr 2015 13:24:50: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8700 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:24:50: #4 Write output xls file... SRX040615.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:24:50: #4 Write peak in narrowPeak format file... SRX040615.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:24:50: #4 Write summits bed file... SRX040615.05_summits.bed INFO @ Tue, 21 Apr 2015 13:24:50: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9759 records, 4 fields): 15 millis CompletedMACS2peakCalling