Job ID = 2162414 sra ファイルのダウンロード中... Completed: 1600834K bytes transferred in 15 seconds (865308K 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 4007 0 4007 0 0 3442 0 --:--:-- 0:00:01 --:--:-- 4118 100 36163 0 36163 0 0 26719 0 --:--:-- 0:00:01 --:--:-- 31121 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 39823483 spots for /home/okishinya/chipatlas/results/dm3/SRX085409/SRR317187.sra Written 39823483 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: 00:08:53 39823483 reads; of these: 39823483 (100.00%) were unpaired; of these: 3414317 (8.57%) aligned 0 times 31783681 (79.81%) aligned exactly 1 time 4625485 (11.61%) aligned >1 times 91.43% 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] 27145944 / 36409166 = 0.7456 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 14:11:13: # Command line: callpeak -t SRX085409.bam -f BAM -g dm -n SRX085409.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX085409.05 # format = BAM # ChIP-seq file = ['SRX085409.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 14:11:13: # Command line: callpeak -t SRX085409.bam -f BAM -g dm -n SRX085409.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX085409.20 # format = BAM # ChIP-seq file = ['SRX085409.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 14:11:13: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:11:13: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:11:13: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:11:13: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:11:13: # Command line: callpeak -t SRX085409.bam -f BAM -g dm -n SRX085409.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX085409.10 # format = BAM # ChIP-seq file = ['SRX085409.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 14:11:13: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:11:13: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:11:19: 1000000 INFO @ Tue, 21 Apr 2015 14:11:19: 1000000 INFO @ Tue, 21 Apr 2015 14:11:19: 1000000 INFO @ Tue, 21 Apr 2015 14:11:24: 2000000 INFO @ Tue, 21 Apr 2015 14:11:25: 2000000 INFO @ Tue, 21 Apr 2015 14:11:25: 2000000 INFO @ Tue, 21 Apr 2015 14:11:30: 3000000 INFO @ Tue, 21 Apr 2015 14:11:31: 3000000 INFO @ Tue, 21 Apr 2015 14:11:31: 3000000 INFO @ Tue, 21 Apr 2015 14:11:36: 4000000 INFO @ Tue, 21 Apr 2015 14:11:37: 4000000 INFO @ Tue, 21 Apr 2015 14:11:37: 4000000 INFO @ Tue, 21 Apr 2015 14:11:42: 5000000 INFO @ Tue, 21 Apr 2015 14:11:43: 5000000 INFO @ Tue, 21 Apr 2015 14:11:43: 5000000 INFO @ Tue, 21 Apr 2015 14:11:47: 6000000 INFO @ Tue, 21 Apr 2015 14:11:50: 6000000 INFO @ Tue, 21 Apr 2015 14:11:50: 6000000 INFO @ Tue, 21 Apr 2015 14:11:53: 7000000 INFO @ Tue, 21 Apr 2015 14:11:56: 7000000 INFO @ Tue, 21 Apr 2015 14:11:56: 7000000 INFO @ Tue, 21 Apr 2015 14:11:59: 8000000 INFO @ Tue, 21 Apr 2015 14:12:02: 8000000 INFO @ Tue, 21 Apr 2015 14:12:02: 8000000 INFO @ Tue, 21 Apr 2015 14:12:05: 9000000 INFO @ Tue, 21 Apr 2015 14:12:06: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 14:12:06: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 14:12:06: #1 total tags in treatment: 9263222 INFO @ Tue, 21 Apr 2015 14:12:06: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:12:06: #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 14:12:08: #1 tags after filtering in treatment: 9261689 INFO @ Tue, 21 Apr 2015 14:12:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:12:08: #1 finished! INFO @ Tue, 21 Apr 2015 14:12:08: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:12:08: 9000000 INFO @ Tue, 21 Apr 2015 14:12:08: 9000000 INFO @ Tue, 21 Apr 2015 14:12:10: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 14:12:10: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 14:12:10: #1 total tags in treatment: 9263222 INFO @ Tue, 21 Apr 2015 14:12:10: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:12:10: #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 14:12:10: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 14:12:10: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 14:12:10: #1 total tags in treatment: 9263222 INFO @ Tue, 21 Apr 2015 14:12:10: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:12:10: #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 14:12:10: #2 number of paired peaks: 4021 INFO @ Tue, 21 Apr 2015 14:12:10: start model_add_line... INFO @ Tue, 21 Apr 2015 14:12:11: #1 tags after filtering in treatment: 9261689 INFO @ Tue, 21 Apr 2015 14:12:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:12:11: #1 finished! INFO @ Tue, 21 Apr 2015 14:12:11: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:12:11: #1 tags after filtering in treatment: 9261689 INFO @ Tue, 21 Apr 2015 14:12:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:12:11: #1 finished! INFO @ Tue, 21 Apr 2015 14:12:11: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:12:13: #2 number of paired peaks: 4021 INFO @ Tue, 21 Apr 2015 14:12:13: start model_add_line... INFO @ Tue, 21 Apr 2015 14:12:13: #2 number of paired peaks: 4021 INFO @ Tue, 21 Apr 2015 14:12:13: start model_add_line... INFO @ Tue, 21 Apr 2015 14:12:36: start X-correlation... INFO @ Tue, 21 Apr 2015 14:12:36: end of X-cor INFO @ Tue, 21 Apr 2015 14:12:36: #2 finished! INFO @ Tue, 21 Apr 2015 14:12:36: #2 predicted fragment length is 121 bps INFO @ Tue, 21 Apr 2015 14:12:36: #2 alternative fragment length(s) may be 121 bps INFO @ Tue, 21 Apr 2015 14:12:36: #2.2 Generate R script for model : SRX085409.10_model.r INFO @ Tue, 21 Apr 2015 14:12:36: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:12:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:12:39: start X-correlation... INFO @ Tue, 21 Apr 2015 14:12:39: end of X-cor INFO @ Tue, 21 Apr 2015 14:12:39: #2 finished! INFO @ Tue, 21 Apr 2015 14:12:39: #2 predicted fragment length is 121 bps INFO @ Tue, 21 Apr 2015 14:12:39: #2 alternative fragment length(s) may be 121 bps INFO @ Tue, 21 Apr 2015 14:12:39: #2.2 Generate R script for model : SRX085409.05_model.r INFO @ Tue, 21 Apr 2015 14:12:39: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:12:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:12:41: start X-correlation... INFO @ Tue, 21 Apr 2015 14:12:41: end of X-cor INFO @ Tue, 21 Apr 2015 14:12:41: #2 finished! INFO @ Tue, 21 Apr 2015 14:12:41: #2 predicted fragment length is 121 bps INFO @ Tue, 21 Apr 2015 14:12:41: #2 alternative fragment length(s) may be 121 bps INFO @ Tue, 21 Apr 2015 14:12:41: #2.2 Generate R script for model : SRX085409.20_model.r INFO @ Tue, 21 Apr 2015 14:12:41: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:12:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:13:28: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:13:31: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:13:34: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:14:11: #4 Write output xls file... SRX085409.10_peaks.xls INFO @ Tue, 21 Apr 2015 14:14:11: #4 Write peak in narrowPeak format file... SRX085409.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:14:11: #4 Write summits bed file... SRX085409.10_summits.bed INFO @ Tue, 21 Apr 2015 14:14:11: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7600 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:14:16: #4 Write output xls file... SRX085409.20_peaks.xls INFO @ Tue, 21 Apr 2015 14:14:16: #4 Write peak in narrowPeak format file... SRX085409.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:14:16: #4 Write summits bed file... SRX085409.20_summits.bed INFO @ Tue, 21 Apr 2015 14:14:16: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5595 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:14:19: #4 Write output xls file... SRX085409.05_peaks.xls INFO @ Tue, 21 Apr 2015 14:14:19: #4 Write peak in narrowPeak format file... SRX085409.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:14:19: #4 Write summits bed file... SRX085409.05_summits.bed INFO @ Tue, 21 Apr 2015 14:14:20: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9978 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。