Job ID = 2161247 sra ファイルのダウンロード中... Completed: 210312K bytes transferred in 5 seconds (327757K 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 23660 0 23660 0 0 33409 0 --:--:-- --:--:-- --:--:-- 45764 100 34474 0 34474 0 0 48619 0 --:--:-- --:--:-- --:--:-- 66552 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 7891078 spots for /home/okishinya/chipatlas/results/dm3/SRX013092/SRR030358.sra Written 7891078 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: 00:01:51 7891078 reads; of these: 7891078 (100.00%) were unpaired; of these: 161709 (2.05%) aligned 0 times 6828978 (86.54%) aligned exactly 1 time 900391 (11.41%) aligned >1 times 97.95% overall alignment rate Time searching: 00:01:51 Overall time: 00:01:51 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] 1417190 / 7729369 = 0.1834 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 12:10:21: # Command line: callpeak -t SRX013092.bam -f BAM -g dm -n SRX013092.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013092.20 # format = BAM # ChIP-seq file = ['SRX013092.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 12:10:21: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:10:21: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:10:21: # Command line: callpeak -t SRX013092.bam -f BAM -g dm -n SRX013092.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013092.10 # format = BAM # ChIP-seq file = ['SRX013092.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 12:10:21: # Command line: callpeak -t SRX013092.bam -f BAM -g dm -n SRX013092.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013092.05 # format = BAM # ChIP-seq file = ['SRX013092.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 12:10:21: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:10:21: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:10:21: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:10:21: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:10:26: 1000000 INFO @ Tue, 21 Apr 2015 12:10:26: 1000000 INFO @ Tue, 21 Apr 2015 12:10:26: 1000000 INFO @ Tue, 21 Apr 2015 12:10:32: 2000000 INFO @ Tue, 21 Apr 2015 12:10:32: 2000000 INFO @ Tue, 21 Apr 2015 12:10:32: 2000000 INFO @ Tue, 21 Apr 2015 12:10:37: 3000000 INFO @ Tue, 21 Apr 2015 12:10:37: 3000000 INFO @ Tue, 21 Apr 2015 12:10:37: 3000000 INFO @ Tue, 21 Apr 2015 12:10:43: 4000000 INFO @ Tue, 21 Apr 2015 12:10:43: 4000000 INFO @ Tue, 21 Apr 2015 12:10:43: 4000000 INFO @ Tue, 21 Apr 2015 12:10:48: 5000000 INFO @ Tue, 21 Apr 2015 12:10:48: 5000000 INFO @ Tue, 21 Apr 2015 12:10:48: 5000000 INFO @ Tue, 21 Apr 2015 12:10:54: 6000000 INFO @ Tue, 21 Apr 2015 12:10:54: 6000000 INFO @ Tue, 21 Apr 2015 12:10:54: 6000000 INFO @ Tue, 21 Apr 2015 12:10:56: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:10:56: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:10:56: #1 total tags in treatment: 6312179 INFO @ Tue, 21 Apr 2015 12:10:56: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:10:56: #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 12:10:56: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:10:56: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:10:56: #1 total tags in treatment: 6312179 INFO @ Tue, 21 Apr 2015 12:10:56: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:10:56: #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 12:10:56: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:10:56: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:10:56: #1 total tags in treatment: 6312179 INFO @ Tue, 21 Apr 2015 12:10:56: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:10:56: #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 12:10:57: #1 tags after filtering in treatment: 6311741 INFO @ Tue, 21 Apr 2015 12:10:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:10:57: #1 finished! INFO @ Tue, 21 Apr 2015 12:10:57: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:10:57: #1 tags after filtering in treatment: 6311741 INFO @ Tue, 21 Apr 2015 12:10:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:10:57: #1 finished! INFO @ Tue, 21 Apr 2015 12:10:57: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:10:57: #1 tags after filtering in treatment: 6311741 INFO @ Tue, 21 Apr 2015 12:10:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:10:57: #1 finished! INFO @ Tue, 21 Apr 2015 12:10:57: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:10:59: #2 number of paired peaks: 5489 INFO @ Tue, 21 Apr 2015 12:10:59: start model_add_line... INFO @ Tue, 21 Apr 2015 12:10:59: #2 number of paired peaks: 5489 INFO @ Tue, 21 Apr 2015 12:10:59: start model_add_line... INFO @ Tue, 21 Apr 2015 12:10:59: #2 number of paired peaks: 5489 INFO @ Tue, 21 Apr 2015 12:10:59: start model_add_line... INFO @ Tue, 21 Apr 2015 12:11:23: start X-correlation... INFO @ Tue, 21 Apr 2015 12:11:23: end of X-cor INFO @ Tue, 21 Apr 2015 12:11:23: #2 finished! INFO @ Tue, 21 Apr 2015 12:11:23: #2 predicted fragment length is 163 bps INFO @ Tue, 21 Apr 2015 12:11:23: #2 alternative fragment length(s) may be 163 bps INFO @ Tue, 21 Apr 2015 12:11:23: #2.2 Generate R script for model : SRX013092.20_model.r INFO @ Tue, 21 Apr 2015 12:11:23: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:11:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:11:24: start X-correlation... INFO @ Tue, 21 Apr 2015 12:11:24: end of X-cor INFO @ Tue, 21 Apr 2015 12:11:24: #2 finished! INFO @ Tue, 21 Apr 2015 12:11:24: #2 predicted fragment length is 163 bps INFO @ Tue, 21 Apr 2015 12:11:24: #2 alternative fragment length(s) may be 163 bps INFO @ Tue, 21 Apr 2015 12:11:24: #2.2 Generate R script for model : SRX013092.05_model.r INFO @ Tue, 21 Apr 2015 12:11:24: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:11:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:11:24: start X-correlation... INFO @ Tue, 21 Apr 2015 12:11:24: end of X-cor INFO @ Tue, 21 Apr 2015 12:11:24: #2 finished! INFO @ Tue, 21 Apr 2015 12:11:24: #2 predicted fragment length is 163 bps INFO @ Tue, 21 Apr 2015 12:11:24: #2 alternative fragment length(s) may be 163 bps INFO @ Tue, 21 Apr 2015 12:11:24: #2.2 Generate R script for model : SRX013092.10_model.r INFO @ Tue, 21 Apr 2015 12:11:24: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:11:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:12:01: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:12:03: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:12:03: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:12:27: #4 Write output xls file... SRX013092.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:12:27: #4 Write peak in narrowPeak format file... SRX013092.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:12:27: #4 Write summits bed file... SRX013092.20_summits.bed INFO @ Tue, 21 Apr 2015 12:12:27: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (211 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:12:29: #4 Write output xls file... SRX013092.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:12:29: #4 Write peak in narrowPeak format file... SRX013092.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:12:29: #4 Write summits bed file... SRX013092.10_summits.bed INFO @ Tue, 21 Apr 2015 12:12:29: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (735 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:12:32: #4 Write output xls file... SRX013092.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:12:32: #4 Write peak in narrowPeak format file... SRX013092.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:12:32: #4 Write summits bed file... SRX013092.05_summits.bed INFO @ Tue, 21 Apr 2015 12:12:32: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (2012 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。