Job ID = 8696832 sra ファイルのダウンロード中... Completed: 196408K bytes transferred in 6 seconds (246793K 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 --:--:-- 0:00:06 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:07 --:--:-- 0 100 22575 0 22575 0 0 2703 0 --:--:-- 0:00:08 --:--:-- 15243 100 31494 0 31494 0 0 3694 0 --:--:-- 0:00:08 --:--:-- 19018 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 17135472 spots for /home/okishinya/chipatlas/results/dm3/SRX110770/SRR388352.sra Written 17135472 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: 00:00:01 Multiseed full-index search: 00:13:29 17135472 reads; of these: 17135472 (100.00%) were unpaired; of these: 3910415 (22.82%) aligned 0 times 7389566 (43.12%) aligned exactly 1 time 5835491 (34.06%) aligned >1 times 77.18% overall alignment rate Time searching: 00:13:30 Overall time: 00:13:30 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] 6765086 / 13225057 = 0.5115 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 @ Fri, 10 Mar 2017 12:15:50: # Command line: callpeak -t SRX110770.bam -f BAM -g dm -n SRX110770.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX110770.20 # format = BAM # ChIP-seq file = ['SRX110770.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 @ Fri, 10 Mar 2017 12:15:50: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:15:50: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:15:50: # Command line: callpeak -t SRX110770.bam -f BAM -g dm -n SRX110770.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX110770.05 # format = BAM # ChIP-seq file = ['SRX110770.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 @ Fri, 10 Mar 2017 12:15:50: # Command line: callpeak -t SRX110770.bam -f BAM -g dm -n SRX110770.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX110770.10 # format = BAM # ChIP-seq file = ['SRX110770.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 @ Fri, 10 Mar 2017 12:15:50: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:15:50: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:15:50: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:15:50: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:15:57: 1000000 INFO @ Fri, 10 Mar 2017 12:15:57: 1000000 INFO @ Fri, 10 Mar 2017 12:16:00: 1000000 INFO @ Fri, 10 Mar 2017 12:16:05: 2000000 INFO @ Fri, 10 Mar 2017 12:16:05: 2000000 INFO @ Fri, 10 Mar 2017 12:16:09: 2000000 INFO @ Fri, 10 Mar 2017 12:16:12: 3000000 INFO @ Fri, 10 Mar 2017 12:16:15: 3000000 INFO @ Fri, 10 Mar 2017 12:16:18: 3000000 INFO @ Fri, 10 Mar 2017 12:16:19: 4000000 INFO @ Fri, 10 Mar 2017 12:16:24: 4000000 INFO @ Fri, 10 Mar 2017 12:16:26: 5000000 INFO @ Fri, 10 Mar 2017 12:16:27: 4000000 INFO @ Fri, 10 Mar 2017 12:16:33: 6000000 INFO @ Fri, 10 Mar 2017 12:16:34: 5000000 INFO @ Fri, 10 Mar 2017 12:16:36: 5000000 INFO @ Fri, 10 Mar 2017 12:16:36: #1 tag size is determined as 18 bps INFO @ Fri, 10 Mar 2017 12:16:36: #1 tag size = 18 INFO @ Fri, 10 Mar 2017 12:16:36: #1 total tags in treatment: 6459971 INFO @ Fri, 10 Mar 2017 12:16:36: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:16:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:16:38: #1 tags after filtering in treatment: 6459971 INFO @ Fri, 10 Mar 2017 12:16:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:16:38: #1 finished! INFO @ Fri, 10 Mar 2017 12:16:38: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:16:40: #2 number of paired peaks: 3814 INFO @ Fri, 10 Mar 2017 12:16:40: start model_add_line... INFO @ Fri, 10 Mar 2017 12:16:44: 6000000 INFO @ Fri, 10 Mar 2017 12:16:45: 6000000 INFO @ Fri, 10 Mar 2017 12:16:48: #1 tag size is determined as 18 bps INFO @ Fri, 10 Mar 2017 12:16:48: #1 tag size = 18 INFO @ Fri, 10 Mar 2017 12:16:48: #1 total tags in treatment: 6459971 INFO @ Fri, 10 Mar 2017 12:16:48: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:16:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:16:49: #1 tag size is determined as 18 bps INFO @ Fri, 10 Mar 2017 12:16:49: #1 tag size = 18 INFO @ Fri, 10 Mar 2017 12:16:49: #1 total tags in treatment: 6459971 INFO @ Fri, 10 Mar 2017 12:16:49: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:16:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:16:50: #1 tags after filtering in treatment: 6459971 INFO @ Fri, 10 Mar 2017 12:16:50: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:16:50: #1 finished! INFO @ Fri, 10 Mar 2017 12:16:50: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:16:51: #1 tags after filtering in treatment: 6459971 INFO @ Fri, 10 Mar 2017 12:16:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:16:51: #1 finished! INFO @ Fri, 10 Mar 2017 12:16:51: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:16:52: #2 number of paired peaks: 3814 INFO @ Fri, 10 Mar 2017 12:16:52: start model_add_line... INFO @ Fri, 10 Mar 2017 12:16:53: #2 number of paired peaks: 3814 INFO @ Fri, 10 Mar 2017 12:16:53: start model_add_line... INFO @ Fri, 10 Mar 2017 12:17:03: start X-correlation... INFO @ Fri, 10 Mar 2017 12:17:03: end of X-cor INFO @ Fri, 10 Mar 2017 12:17:03: #2 finished! INFO @ Fri, 10 Mar 2017 12:17:03: #2 predicted fragment length is 89 bps INFO @ Fri, 10 Mar 2017 12:17:03: #2 alternative fragment length(s) may be 89 bps INFO @ Fri, 10 Mar 2017 12:17:03: #2.2 Generate R script for model : SRX110770.05_model.r INFO @ Fri, 10 Mar 2017 12:17:03: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:17:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:17:14: start X-correlation... INFO @ Fri, 10 Mar 2017 12:17:14: end of X-cor INFO @ Fri, 10 Mar 2017 12:17:14: #2 finished! INFO @ Fri, 10 Mar 2017 12:17:14: #2 predicted fragment length is 89 bps INFO @ Fri, 10 Mar 2017 12:17:14: #2 alternative fragment length(s) may be 89 bps INFO @ Fri, 10 Mar 2017 12:17:14: #2.2 Generate R script for model : SRX110770.10_model.r INFO @ Fri, 10 Mar 2017 12:17:14: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:17:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:17:15: start X-correlation... INFO @ Fri, 10 Mar 2017 12:17:15: end of X-cor INFO @ Fri, 10 Mar 2017 12:17:15: #2 finished! INFO @ Fri, 10 Mar 2017 12:17:15: #2 predicted fragment length is 89 bps INFO @ Fri, 10 Mar 2017 12:17:15: #2 alternative fragment length(s) may be 89 bps INFO @ Fri, 10 Mar 2017 12:17:15: #2.2 Generate R script for model : SRX110770.20_model.r INFO @ Fri, 10 Mar 2017 12:17:15: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:17:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:17:50: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:18:01: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:18:01: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:18:32: #4 Write output xls file... SRX110770.05_peaks.xls INFO @ Fri, 10 Mar 2017 12:18:33: #4 Write peak in narrowPeak format file... SRX110770.05_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:18:33: #4 Write summits bed file... SRX110770.05_summits.bed INFO @ Fri, 10 Mar 2017 12:18:33: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (7809 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 12:18:36: #4 Write output xls file... SRX110770.20_peaks.xls INFO @ Fri, 10 Mar 2017 12:18:36: #4 Write peak in narrowPeak format file... SRX110770.20_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:18:36: #4 Write summits bed file... SRX110770.20_summits.bed INFO @ Fri, 10 Mar 2017 12:18:36: Done! pass1 - making usageList (12 chroms): 3 millis pass2 - checking and writing primary data (4279 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 12:18:39: #4 Write output xls file... SRX110770.10_peaks.xls INFO @ Fri, 10 Mar 2017 12:18:39: #4 Write peak in narrowPeak format file... SRX110770.10_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:18:39: #4 Write summits bed file... SRX110770.10_summits.bed INFO @ Fri, 10 Mar 2017 12:18:39: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5966 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。