Job ID = 2161570 sra ファイルのダウンロード中... Completed: 956596K bytes transferred in 9 seconds (845415K bits/sec), in 2 files, 3 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 16368 0 16368 0 0 21771 0 --:--:-- --:--:-- --:--:-- 29176 100 45307 0 45307 0 0 48124 0 --:--:-- --:--:-- --:--:-- 60328 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 22252217 spots for /home/okishinya/chipatlas/results/dm3/SRX030964/SRR072394.sra Written 22252217 spots total Written 23804585 spots for /home/okishinya/chipatlas/results/dm3/SRX030964/SRR072393.sra Written 23804585 spots total 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:52 46056802 reads; of these: 46056802 (100.00%) were unpaired; of these: 13381683 (29.05%) aligned 0 times 28073762 (60.95%) aligned exactly 1 time 4601357 (9.99%) aligned >1 times 70.95% overall alignment rate Time searching: 00:08:53 Overall time: 00:08:53 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 12 files... [bam_rmdupse_core] 21801378 / 32675119 = 0.6672 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 13:08:18: # Command line: callpeak -t SRX030964.bam -f BAM -g dm -n SRX030964.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX030964.10 # format = BAM # ChIP-seq file = ['SRX030964.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 13:08:18: # Command line: callpeak -t SRX030964.bam -f BAM -g dm -n SRX030964.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX030964.05 # format = BAM # ChIP-seq file = ['SRX030964.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 13:08:18: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:08:18: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:08:18: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:08:18: # Command line: callpeak -t SRX030964.bam -f BAM -g dm -n SRX030964.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX030964.20 # format = BAM # ChIP-seq file = ['SRX030964.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 13:08:18: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:08:18: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:08:18: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:08:24: 1000000 INFO @ Tue, 21 Apr 2015 13:08:24: 1000000 INFO @ Tue, 21 Apr 2015 13:08:24: 1000000 INFO @ Tue, 21 Apr 2015 13:08:30: 2000000 INFO @ Tue, 21 Apr 2015 13:08:30: 2000000 INFO @ Tue, 21 Apr 2015 13:08:31: 2000000 INFO @ Tue, 21 Apr 2015 13:08:36: 3000000 INFO @ Tue, 21 Apr 2015 13:08:37: 3000000 INFO @ Tue, 21 Apr 2015 13:08:37: 3000000 INFO @ Tue, 21 Apr 2015 13:08:42: 4000000 INFO @ Tue, 21 Apr 2015 13:08:43: 4000000 INFO @ Tue, 21 Apr 2015 13:08:44: 4000000 INFO @ Tue, 21 Apr 2015 13:08:49: 5000000 INFO @ Tue, 21 Apr 2015 13:08:49: 5000000 INFO @ Tue, 21 Apr 2015 13:08:50: 5000000 INFO @ Tue, 21 Apr 2015 13:08:55: 6000000 INFO @ Tue, 21 Apr 2015 13:08:55: 6000000 INFO @ Tue, 21 Apr 2015 13:08:57: 6000000 INFO @ Tue, 21 Apr 2015 13:09:01: 7000000 INFO @ Tue, 21 Apr 2015 13:09:02: 7000000 INFO @ Tue, 21 Apr 2015 13:09:04: 7000000 INFO @ Tue, 21 Apr 2015 13:09:07: 8000000 INFO @ Tue, 21 Apr 2015 13:09:08: 8000000 INFO @ Tue, 21 Apr 2015 13:09:11: 8000000 INFO @ Tue, 21 Apr 2015 13:09:14: 9000000 INFO @ Tue, 21 Apr 2015 13:09:15: 9000000 INFO @ Tue, 21 Apr 2015 13:09:18: 9000000 INFO @ Tue, 21 Apr 2015 13:09:21: 10000000 INFO @ Tue, 21 Apr 2015 13:09:22: 10000000 INFO @ Tue, 21 Apr 2015 13:09:25: 10000000 INFO @ Tue, 21 Apr 2015 13:09:27: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:09:27: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:09:27: #1 total tags in treatment: 10873741 INFO @ Tue, 21 Apr 2015 13:09:27: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:09:27: #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 13:09:28: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:09:28: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:09:28: #1 total tags in treatment: 10873741 INFO @ Tue, 21 Apr 2015 13:09:28: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:09:28: #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 13:09:29: #1 tags after filtering in treatment: 10871853 INFO @ Tue, 21 Apr 2015 13:09:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:09:29: #1 finished! INFO @ Tue, 21 Apr 2015 13:09:29: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:09:30: #1 tags after filtering in treatment: 10871853 INFO @ Tue, 21 Apr 2015 13:09:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:09:30: #1 finished! INFO @ Tue, 21 Apr 2015 13:09:30: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:09:30: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:09:30: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:09:30: #1 total tags in treatment: 10873741 INFO @ Tue, 21 Apr 2015 13:09:30: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:09:30: #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 13:09:31: #2 number of paired peaks: 1141 INFO @ Tue, 21 Apr 2015 13:09:31: start model_add_line... INFO @ Tue, 21 Apr 2015 13:09:32: #2 number of paired peaks: 1141 INFO @ Tue, 21 Apr 2015 13:09:32: start model_add_line... INFO @ Tue, 21 Apr 2015 13:09:32: #1 tags after filtering in treatment: 10871853 INFO @ Tue, 21 Apr 2015 13:09:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:09:32: #1 finished! INFO @ Tue, 21 Apr 2015 13:09:32: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:09:34: #2 number of paired peaks: 1141 INFO @ Tue, 21 Apr 2015 13:09:34: start model_add_line... INFO @ Tue, 21 Apr 2015 13:09:40: start X-correlation... INFO @ Tue, 21 Apr 2015 13:09:40: end of X-cor INFO @ Tue, 21 Apr 2015 13:09:40: #2 finished! INFO @ Tue, 21 Apr 2015 13:09:40: #2 predicted fragment length is 323 bps INFO @ Tue, 21 Apr 2015 13:09:40: #2 alternative fragment length(s) may be 323 bps INFO @ Tue, 21 Apr 2015 13:09:40: #2.2 Generate R script for model : SRX030964.05_model.r INFO @ Tue, 21 Apr 2015 13:09:40: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:09:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:09:41: start X-correlation... INFO @ Tue, 21 Apr 2015 13:09:41: end of X-cor INFO @ Tue, 21 Apr 2015 13:09:41: #2 finished! INFO @ Tue, 21 Apr 2015 13:09:41: #2 predicted fragment length is 323 bps INFO @ Tue, 21 Apr 2015 13:09:41: #2 alternative fragment length(s) may be 323 bps INFO @ Tue, 21 Apr 2015 13:09:41: #2.2 Generate R script for model : SRX030964.10_model.r INFO @ Tue, 21 Apr 2015 13:09:41: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:09:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:09:43: start X-correlation... INFO @ Tue, 21 Apr 2015 13:09:43: end of X-cor INFO @ Tue, 21 Apr 2015 13:09:43: #2 finished! INFO @ Tue, 21 Apr 2015 13:09:43: #2 predicted fragment length is 323 bps INFO @ Tue, 21 Apr 2015 13:09:43: #2 alternative fragment length(s) may be 323 bps INFO @ Tue, 21 Apr 2015 13:09:43: #2.2 Generate R script for model : SRX030964.20_model.r INFO @ Tue, 21 Apr 2015 13:09:43: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:09:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:10:47: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:10:50: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:10:52: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:11:39: #4 Write output xls file... SRX030964.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:11:39: #4 Write peak in narrowPeak format file... SRX030964.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:11:39: #4 Write summits bed file... SRX030964.20_summits.bed INFO @ Tue, 21 Apr 2015 13:11:39: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1722 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:11:42: #4 Write output xls file... SRX030964.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:11:42: #4 Write peak in narrowPeak format file... SRX030964.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:11:42: #4 Write summits bed file... SRX030964.10_summits.bed INFO @ Tue, 21 Apr 2015 13:11:42: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3912 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:11:43: #4 Write output xls file... SRX030964.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:11:44: #4 Write peak in narrowPeak format file... SRX030964.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:11:44: #4 Write summits bed file... SRX030964.05_summits.bed INFO @ Tue, 21 Apr 2015 13:11:44: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6457 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。