Job ID = 2161558 sra ファイルのダウンロード中... Completed: 8561850K bytes transferred in 93 seconds (748511K 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 13456 0 13456 0 0 25077 0 --:--:-- --:--:-- --:--:-- 38890 100 37048 0 37048 0 0 51020 0 --:--:-- --:--:-- --:--:-- 69119 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 13975739 spots for /home/okishinya/chipatlas/results/dm3/SRX027833/SRR067916.sra Written 13975739 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: 00:03:03 13975739 reads; of these: 13975739 (100.00%) were unpaired; of these: 5242743 (37.51%) aligned 0 times 6520201 (46.65%) aligned exactly 1 time 2212795 (15.83%) aligned >1 times 62.49% overall alignment rate Time searching: 00:03:03 Overall time: 00:03:03 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] 1148872 / 8732996 = 0.1316 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 12:54:11: # Command line: callpeak -t SRX027833.bam -f BAM -g dm -n SRX027833.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX027833.05 # format = BAM # ChIP-seq file = ['SRX027833.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 12:54:11: # Command line: callpeak -t SRX027833.bam -f BAM -g dm -n SRX027833.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX027833.20 # format = BAM # ChIP-seq file = ['SRX027833.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 12:54:11: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:54:11: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:54:11: # Command line: callpeak -t SRX027833.bam -f BAM -g dm -n SRX027833.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX027833.10 # format = BAM # ChIP-seq file = ['SRX027833.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 12:54:11: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:54:11: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:54:11: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:54:11: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:54:16: 1000000 INFO @ Tue, 21 Apr 2015 12:54:17: 1000000 INFO @ Tue, 21 Apr 2015 12:54:17: 1000000 INFO @ Tue, 21 Apr 2015 12:54:22: 2000000 INFO @ Tue, 21 Apr 2015 12:54:23: 2000000 INFO @ Tue, 21 Apr 2015 12:54:23: 2000000 INFO @ Tue, 21 Apr 2015 12:54:27: 3000000 INFO @ Tue, 21 Apr 2015 12:54:28: 3000000 INFO @ Tue, 21 Apr 2015 12:54:28: 3000000 INFO @ Tue, 21 Apr 2015 12:54:32: 4000000 INFO @ Tue, 21 Apr 2015 12:54:33: 4000000 INFO @ Tue, 21 Apr 2015 12:54:34: 4000000 INFO @ Tue, 21 Apr 2015 12:54:37: 5000000 INFO @ Tue, 21 Apr 2015 12:54:38: 5000000 INFO @ Tue, 21 Apr 2015 12:54:40: 5000000 INFO @ Tue, 21 Apr 2015 12:54:42: 6000000 INFO @ Tue, 21 Apr 2015 12:54:43: 6000000 INFO @ Tue, 21 Apr 2015 12:54:45: 6000000 INFO @ Tue, 21 Apr 2015 12:54:47: 7000000 INFO @ Tue, 21 Apr 2015 12:54:49: 7000000 INFO @ Tue, 21 Apr 2015 12:54:50: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:54:50: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:54:50: #1 total tags in treatment: 7584124 INFO @ Tue, 21 Apr 2015 12:54:50: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:54:50: #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 12:54:51: 7000000 INFO @ Tue, 21 Apr 2015 12:54:52: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:54:52: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:54:52: #1 total tags in treatment: 7584124 INFO @ Tue, 21 Apr 2015 12:54:52: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:54:52: #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 12:54:52: #1 tags after filtering in treatment: 7583343 INFO @ Tue, 21 Apr 2015 12:54:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:54:52: #1 finished! INFO @ Tue, 21 Apr 2015 12:54:52: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:54:53: #1 tags after filtering in treatment: 7583343 INFO @ Tue, 21 Apr 2015 12:54:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:54:53: #1 finished! INFO @ Tue, 21 Apr 2015 12:54:53: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:54:54: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:54:54: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:54:54: #1 total tags in treatment: 7584124 INFO @ Tue, 21 Apr 2015 12:54:54: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:54:54: #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 12:54:54: #2 number of paired peaks: 5466 INFO @ Tue, 21 Apr 2015 12:54:54: start model_add_line... INFO @ Tue, 21 Apr 2015 12:54:55: #2 number of paired peaks: 5466 INFO @ Tue, 21 Apr 2015 12:54:55: start model_add_line... INFO @ Tue, 21 Apr 2015 12:54:55: #1 tags after filtering in treatment: 7583343 INFO @ Tue, 21 Apr 2015 12:54:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:54:55: #1 finished! INFO @ Tue, 21 Apr 2015 12:54:55: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:54:57: #2 number of paired peaks: 5466 INFO @ Tue, 21 Apr 2015 12:54:57: start model_add_line... INFO @ Tue, 21 Apr 2015 12:55:20: start X-correlation... INFO @ Tue, 21 Apr 2015 12:55:20: end of X-cor INFO @ Tue, 21 Apr 2015 12:55:20: #2 finished! INFO @ Tue, 21 Apr 2015 12:55:20: #2 predicted fragment length is 92 bps INFO @ Tue, 21 Apr 2015 12:55:20: #2 alternative fragment length(s) may be 92 bps INFO @ Tue, 21 Apr 2015 12:55:20: #2.2 Generate R script for model : SRX027833.20_model.r INFO @ Tue, 21 Apr 2015 12:55:20: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:55:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:55:20: start X-correlation... INFO @ Tue, 21 Apr 2015 12:55:20: end of X-cor INFO @ Tue, 21 Apr 2015 12:55:20: #2 finished! INFO @ Tue, 21 Apr 2015 12:55:20: #2 predicted fragment length is 92 bps INFO @ Tue, 21 Apr 2015 12:55:20: #2 alternative fragment length(s) may be 92 bps INFO @ Tue, 21 Apr 2015 12:55:20: #2.2 Generate R script for model : SRX027833.05_model.r INFO @ Tue, 21 Apr 2015 12:55:20: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:55:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:55:23: start X-correlation... INFO @ Tue, 21 Apr 2015 12:55:23: end of X-cor INFO @ Tue, 21 Apr 2015 12:55:23: #2 finished! INFO @ Tue, 21 Apr 2015 12:55:23: #2 predicted fragment length is 92 bps INFO @ Tue, 21 Apr 2015 12:55:23: #2 alternative fragment length(s) may be 92 bps INFO @ Tue, 21 Apr 2015 12:55:23: #2.2 Generate R script for model : SRX027833.10_model.r INFO @ Tue, 21 Apr 2015 12:55:23: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:55:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:56:01: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:56:01: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:56:05: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:56:34: #4 Write output xls file... SRX027833.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:56:34: #4 Write peak in narrowPeak format file... SRX027833.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:56:34: #4 Write summits bed file... SRX027833.20_summits.bed INFO @ Tue, 21 Apr 2015 12:56:34: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4765 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:56:43: #4 Write output xls file... SRX027833.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:56:43: #4 Write peak in narrowPeak format file... SRX027833.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:56:44: #4 Write summits bed file... SRX027833.10_summits.bed INFO @ Tue, 21 Apr 2015 12:56:44: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (9194 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:56:44: #4 Write output xls file... SRX027833.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:56:44: #4 Write peak in narrowPeak format file... SRX027833.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:56:44: #4 Write summits bed file... SRX027833.05_summits.bed INFO @ Tue, 21 Apr 2015 12:56:44: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (11401 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。