Job ID = 2162413 sra ファイルのダウンロード中... Completed: 1627080K bytes transferred in 16 seconds (792464K 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 4000 0 4000 0 0 3396 0 --:--:-- 0:00:01 --:--:-- 4052 100 36157 0 36157 0 0 26444 0 --:--:-- 0:00:01 --:--:-- 30771 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 39793560 spots for /home/okishinya/chipatlas/results/dm3/SRX085408/SRR317186.sra Written 39793560 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: 00:08:59 39793560 reads; of these: 39793560 (100.00%) were unpaired; of these: 4610143 (11.59%) aligned 0 times 30571314 (76.82%) aligned exactly 1 time 4612103 (11.59%) aligned >1 times 88.41% overall alignment rate Time searching: 00:08:59 Overall time: 00:08:59 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] 26469139 / 35183417 = 0.7523 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 14:10:49: # Command line: callpeak -t SRX085408.bam -f BAM -g dm -n SRX085408.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX085408.05 # format = BAM # ChIP-seq file = ['SRX085408.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 14:10:49: # Command line: callpeak -t SRX085408.bam -f BAM -g dm -n SRX085408.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX085408.20 # format = BAM # ChIP-seq file = ['SRX085408.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 14:10:49: # Command line: callpeak -t SRX085408.bam -f BAM -g dm -n SRX085408.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX085408.10 # format = BAM # ChIP-seq file = ['SRX085408.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 14:10:49: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:10:49: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:10:49: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:10:49: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:10:49: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:10:49: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:10:54: 1000000 INFO @ Tue, 21 Apr 2015 14:10:54: 1000000 INFO @ Tue, 21 Apr 2015 14:10:54: 1000000 INFO @ Tue, 21 Apr 2015 14:10:59: 2000000 INFO @ Tue, 21 Apr 2015 14:10:59: 2000000 INFO @ Tue, 21 Apr 2015 14:10:59: 2000000 INFO @ Tue, 21 Apr 2015 14:11:03: 3000000 INFO @ Tue, 21 Apr 2015 14:11:04: 3000000 INFO @ Tue, 21 Apr 2015 14:11:04: 3000000 INFO @ Tue, 21 Apr 2015 14:11:08: 4000000 INFO @ Tue, 21 Apr 2015 14:11:09: 4000000 INFO @ Tue, 21 Apr 2015 14:11:09: 4000000 INFO @ Tue, 21 Apr 2015 14:11:13: 5000000 INFO @ Tue, 21 Apr 2015 14:11:14: 5000000 INFO @ Tue, 21 Apr 2015 14:11:14: 5000000 INFO @ Tue, 21 Apr 2015 14:11:18: 6000000 INFO @ Tue, 21 Apr 2015 14:11:19: 6000000 INFO @ Tue, 21 Apr 2015 14:11:19: 6000000 INFO @ Tue, 21 Apr 2015 14:11:23: 7000000 INFO @ Tue, 21 Apr 2015 14:11:24: 7000000 INFO @ Tue, 21 Apr 2015 14:11:24: 7000000 INFO @ Tue, 21 Apr 2015 14:11:28: 8000000 INFO @ Tue, 21 Apr 2015 14:11:29: 8000000 INFO @ Tue, 21 Apr 2015 14:11:29: 8000000 INFO @ Tue, 21 Apr 2015 14:11:31: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 14:11:31: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 14:11:31: #1 total tags in treatment: 8714278 INFO @ Tue, 21 Apr 2015 14:11:31: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:11:31: #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 14:11:33: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 14:11:33: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 14:11:33: #1 total tags in treatment: 8714278 INFO @ Tue, 21 Apr 2015 14:11:33: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:11:33: #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 14:11:33: #1 tags after filtering in treatment: 8712614 INFO @ Tue, 21 Apr 2015 14:11:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:11:33: #1 finished! INFO @ Tue, 21 Apr 2015 14:11:33: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:11:33: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 14:11:33: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 14:11:33: #1 total tags in treatment: 8714278 INFO @ Tue, 21 Apr 2015 14:11:33: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:11:33: #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 14:11:34: #1 tags after filtering in treatment: 8712614 INFO @ Tue, 21 Apr 2015 14:11:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:11:34: #1 finished! INFO @ Tue, 21 Apr 2015 14:11:34: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:11:35: #1 tags after filtering in treatment: 8712614 INFO @ Tue, 21 Apr 2015 14:11:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:11:35: #1 finished! INFO @ Tue, 21 Apr 2015 14:11:35: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:11:35: #2 number of paired peaks: 4114 INFO @ Tue, 21 Apr 2015 14:11:35: start model_add_line... INFO @ Tue, 21 Apr 2015 14:11:36: #2 number of paired peaks: 4114 INFO @ Tue, 21 Apr 2015 14:11:36: start model_add_line... INFO @ Tue, 21 Apr 2015 14:11:37: #2 number of paired peaks: 4114 INFO @ Tue, 21 Apr 2015 14:11:37: start model_add_line... INFO @ Tue, 21 Apr 2015 14:12:00: start X-correlation... INFO @ Tue, 21 Apr 2015 14:12:00: end of X-cor INFO @ Tue, 21 Apr 2015 14:12:00: #2 finished! INFO @ Tue, 21 Apr 2015 14:12:00: #2 predicted fragment length is 115 bps INFO @ Tue, 21 Apr 2015 14:12:00: #2 alternative fragment length(s) may be 115 bps INFO @ Tue, 21 Apr 2015 14:12:00: #2.2 Generate R script for model : SRX085408.05_model.r INFO @ Tue, 21 Apr 2015 14:12:00: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:12:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:12:01: start X-correlation... INFO @ Tue, 21 Apr 2015 14:12:01: end of X-cor INFO @ Tue, 21 Apr 2015 14:12:01: #2 finished! INFO @ Tue, 21 Apr 2015 14:12:01: #2 predicted fragment length is 115 bps INFO @ Tue, 21 Apr 2015 14:12:01: #2 alternative fragment length(s) may be 115 bps INFO @ Tue, 21 Apr 2015 14:12:01: #2.2 Generate R script for model : SRX085408.10_model.r INFO @ Tue, 21 Apr 2015 14:12:01: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:12:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:12:02: start X-correlation... INFO @ Tue, 21 Apr 2015 14:12:02: end of X-cor INFO @ Tue, 21 Apr 2015 14:12:02: #2 finished! INFO @ Tue, 21 Apr 2015 14:12:02: #2 predicted fragment length is 115 bps INFO @ Tue, 21 Apr 2015 14:12:02: #2 alternative fragment length(s) may be 115 bps INFO @ Tue, 21 Apr 2015 14:12:02: #2.2 Generate R script for model : SRX085408.20_model.r INFO @ Tue, 21 Apr 2015 14:12:02: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:12:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:12:48: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:12:50: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:12:52: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:13:28: #4 Write output xls file... SRX085408.20_peaks.xls INFO @ Tue, 21 Apr 2015 14:13:28: #4 Write peak in narrowPeak format file... SRX085408.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:13:28: #4 Write summits bed file... SRX085408.20_summits.bed INFO @ Tue, 21 Apr 2015 14:13:28: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5627 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:13:32: #4 Write output xls file... SRX085408.05_peaks.xls INFO @ Tue, 21 Apr 2015 14:13:33: #4 Write peak in narrowPeak format file... SRX085408.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:13:33: #4 Write summits bed file... SRX085408.05_summits.bed INFO @ Tue, 21 Apr 2015 14:13:33: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9884 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:13:34: #4 Write output xls file... SRX085408.10_peaks.xls INFO @ Tue, 21 Apr 2015 14:13:34: #4 Write peak in narrowPeak format file... SRX085408.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:13:35: #4 Write summits bed file... SRX085408.10_summits.bed INFO @ Tue, 21 Apr 2015 14:13:35: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7568 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。