Job ID = 2161546 sra ファイルのダウンロード中... Completed: 158768K bytes transferred in 4 seconds (271932K 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 35937 0 35937 0 0 44460 0 --:--:-- --:--:-- --:--:-- 58244 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 6999600 spots for /home/okishinya/chipatlas/results/dm3/SRX027391/SRR066836.sra Written 6999600 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: 00:01:27 6999600 reads; of these: 6999600 (100.00%) were unpaired; of these: 505443 (7.22%) aligned 0 times 5944042 (84.92%) aligned exactly 1 time 550115 (7.86%) aligned >1 times 92.78% overall alignment rate Time searching: 00:01:27 Overall time: 00:01:27 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 628763 / 6494157 = 0.0968 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 12:47:47: # Command line: callpeak -t SRX027391.bam -f BAM -g dm -n SRX027391.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX027391.10 # format = BAM # ChIP-seq file = ['SRX027391.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 12:47:47: # Command line: callpeak -t SRX027391.bam -f BAM -g dm -n SRX027391.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX027391.05 # format = BAM # ChIP-seq file = ['SRX027391.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 12:47:47: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:47:47: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:47:47: # Command line: callpeak -t SRX027391.bam -f BAM -g dm -n SRX027391.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX027391.20 # format = BAM # ChIP-seq file = ['SRX027391.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 12:47:47: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:47:47: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:47:47: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:47:47: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:47:52: 1000000 INFO @ Tue, 21 Apr 2015 12:47:52: 1000000 INFO @ Tue, 21 Apr 2015 12:47:52: 1000000 INFO @ Tue, 21 Apr 2015 12:47:57: 2000000 INFO @ Tue, 21 Apr 2015 12:47:57: 2000000 INFO @ Tue, 21 Apr 2015 12:47:57: 2000000 INFO @ Tue, 21 Apr 2015 12:48:02: 3000000 INFO @ Tue, 21 Apr 2015 12:48:02: 3000000 INFO @ Tue, 21 Apr 2015 12:48:02: 3000000 INFO @ Tue, 21 Apr 2015 12:48:07: 4000000 INFO @ Tue, 21 Apr 2015 12:48:07: 4000000 INFO @ Tue, 21 Apr 2015 12:48:08: 4000000 INFO @ Tue, 21 Apr 2015 12:48:12: 5000000 INFO @ Tue, 21 Apr 2015 12:48:13: 5000000 INFO @ Tue, 21 Apr 2015 12:48:14: 5000000 INFO @ Tue, 21 Apr 2015 12:48:17: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:48:17: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:48:17: #1 total tags in treatment: 5865394 INFO @ Tue, 21 Apr 2015 12:48:17: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:48:17: #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 12:48:17: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:48:17: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:48:17: #1 total tags in treatment: 5865394 INFO @ Tue, 21 Apr 2015 12:48:17: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:48:17: #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 12:48:18: #1 tags after filtering in treatment: 5865173 INFO @ Tue, 21 Apr 2015 12:48:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:48:18: #1 finished! INFO @ Tue, 21 Apr 2015 12:48:18: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:48:18: #1 tags after filtering in treatment: 5865173 INFO @ Tue, 21 Apr 2015 12:48:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:48:18: #1 finished! INFO @ Tue, 21 Apr 2015 12:48:18: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:48:18: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:48:18: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:48:18: #1 total tags in treatment: 5865394 INFO @ Tue, 21 Apr 2015 12:48:18: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:48:18: #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 12:48:19: #2 number of paired peaks: 2633 INFO @ Tue, 21 Apr 2015 12:48:19: start model_add_line... INFO @ Tue, 21 Apr 2015 12:48:19: #1 tags after filtering in treatment: 5865173 INFO @ Tue, 21 Apr 2015 12:48:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:48:19: #1 finished! INFO @ Tue, 21 Apr 2015 12:48:19: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:48:19: #2 number of paired peaks: 2633 INFO @ Tue, 21 Apr 2015 12:48:19: start model_add_line... INFO @ Tue, 21 Apr 2015 12:48:21: #2 number of paired peaks: 2633 INFO @ Tue, 21 Apr 2015 12:48:21: start model_add_line... INFO @ Tue, 21 Apr 2015 12:48:27: start X-correlation... INFO @ Tue, 21 Apr 2015 12:48:27: end of X-cor INFO @ Tue, 21 Apr 2015 12:48:27: #2 finished! INFO @ Tue, 21 Apr 2015 12:48:27: #2 predicted fragment length is 121 bps INFO @ Tue, 21 Apr 2015 12:48:27: #2 alternative fragment length(s) may be 121 bps INFO @ Tue, 21 Apr 2015 12:48:27: #2.2 Generate R script for model : SRX027391.20_model.r INFO @ Tue, 21 Apr 2015 12:48:27: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:48:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:48:27: start X-correlation... INFO @ Tue, 21 Apr 2015 12:48:27: end of X-cor INFO @ Tue, 21 Apr 2015 12:48:27: #2 finished! INFO @ Tue, 21 Apr 2015 12:48:27: #2 predicted fragment length is 121 bps INFO @ Tue, 21 Apr 2015 12:48:27: #2 alternative fragment length(s) may be 121 bps INFO @ Tue, 21 Apr 2015 12:48:27: #2.2 Generate R script for model : SRX027391.05_model.r INFO @ Tue, 21 Apr 2015 12:48:27: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:48:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:48:29: start X-correlation... INFO @ Tue, 21 Apr 2015 12:48:29: end of X-cor INFO @ Tue, 21 Apr 2015 12:48:29: #2 finished! INFO @ Tue, 21 Apr 2015 12:48:29: #2 predicted fragment length is 121 bps INFO @ Tue, 21 Apr 2015 12:48:29: #2 alternative fragment length(s) may be 121 bps INFO @ Tue, 21 Apr 2015 12:48:29: #2.2 Generate R script for model : SRX027391.10_model.r INFO @ Tue, 21 Apr 2015 12:48:29: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:48:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:48:59: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:49:00: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:49:03: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:49:24: #4 Write output xls file... SRX027391.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:49:24: #4 Write peak in narrowPeak format file... SRX027391.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:49:24: #4 Write summits bed file... SRX027391.20_summits.bed INFO @ Tue, 21 Apr 2015 12:49:24: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (2032 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:49:34: #4 Write output xls file... SRX027391.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:49:34: #4 Write peak in narrowPeak format file... SRX027391.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:49:34: #4 Write summits bed file... SRX027391.10_summits.bed INFO @ Tue, 21 Apr 2015 12:49:34: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (7911 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:49:38: #4 Write output xls file... SRX027391.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:49:39: #4 Write peak in narrowPeak format file... SRX027391.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:49:39: #4 Write summits bed file... SRX027391.05_summits.bed INFO @ Tue, 21 Apr 2015 12:49:39: Done! pass1 - making usageList (13 chroms): 4 millis pass2 - checking and writing primary data (19351 records, 4 fields): 23 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。