Job ID = 2161424 sra ファイルのダウンロード中... Completed: 205598K bytes transferred in 5 seconds (329261K 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 29814 0 29814 0 0 39514 0 --:--:-- --:--:-- --:--:-- 52861 100 35819 0 35819 0 0 47420 0 --:--:-- --:--:-- --:--:-- 63396 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 7293970 spots for /home/okishinya/chipatlas/results/dm3/SRX026742/SRR065628.sra Written 7293970 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: 00:01:35 7293970 reads; of these: 7293970 (100.00%) were unpaired; of these: 1315931 (18.04%) aligned 0 times 5205430 (71.37%) aligned exactly 1 time 772609 (10.59%) aligned >1 times 81.96% overall alignment rate Time searching: 00:01:35 Overall time: 00:01:36 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] 2011618 / 5978039 = 0.3365 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 12:40:39: # Command line: callpeak -t SRX026742.bam -f BAM -g dm -n SRX026742.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX026742.10 # format = BAM # ChIP-seq file = ['SRX026742.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 12:40:39: # Command line: callpeak -t SRX026742.bam -f BAM -g dm -n SRX026742.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX026742.20 # format = BAM # ChIP-seq file = ['SRX026742.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 12:40:39: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:40:39: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:40:39: # Command line: callpeak -t SRX026742.bam -f BAM -g dm -n SRX026742.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX026742.05 # format = BAM # ChIP-seq file = ['SRX026742.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 12:40:39: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:40:39: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:40:39: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:40:39: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:40:44: 1000000 INFO @ Tue, 21 Apr 2015 12:40:44: 1000000 INFO @ Tue, 21 Apr 2015 12:40:44: 1000000 INFO @ Tue, 21 Apr 2015 12:40:49: 2000000 INFO @ Tue, 21 Apr 2015 12:40:50: 2000000 INFO @ Tue, 21 Apr 2015 12:40:50: 2000000 INFO @ Tue, 21 Apr 2015 12:40:55: 3000000 INFO @ Tue, 21 Apr 2015 12:40:55: 3000000 INFO @ Tue, 21 Apr 2015 12:40:56: 3000000 INFO @ Tue, 21 Apr 2015 12:41:01: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 12:41:01: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 12:41:01: #1 total tags in treatment: 3966421 INFO @ Tue, 21 Apr 2015 12:41:01: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:41:01: #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 12:41:01: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 12:41:01: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 12:41:01: #1 total tags in treatment: 3966421 INFO @ Tue, 21 Apr 2015 12:41:01: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:41:01: #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 12:41:02: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 12:41:02: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 12:41:02: #1 total tags in treatment: 3966421 INFO @ Tue, 21 Apr 2015 12:41:02: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:41:02: #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 12:41:02: #1 tags after filtering in treatment: 3966089 INFO @ Tue, 21 Apr 2015 12:41:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:41:02: #1 finished! INFO @ Tue, 21 Apr 2015 12:41:02: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:41:02: #1 tags after filtering in treatment: 3966089 INFO @ Tue, 21 Apr 2015 12:41:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:41:02: #1 finished! INFO @ Tue, 21 Apr 2015 12:41:02: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:41:03: #1 tags after filtering in treatment: 3966089 INFO @ Tue, 21 Apr 2015 12:41:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:41:03: #1 finished! INFO @ Tue, 21 Apr 2015 12:41:03: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:41:03: #2 number of paired peaks: 5857 INFO @ Tue, 21 Apr 2015 12:41:03: start model_add_line... INFO @ Tue, 21 Apr 2015 12:41:03: #2 number of paired peaks: 5857 INFO @ Tue, 21 Apr 2015 12:41:03: start model_add_line... INFO @ Tue, 21 Apr 2015 12:41:04: #2 number of paired peaks: 5857 INFO @ Tue, 21 Apr 2015 12:41:04: start model_add_line... INFO @ Tue, 21 Apr 2015 12:41:15: start X-correlation... INFO @ Tue, 21 Apr 2015 12:41:15: end of X-cor INFO @ Tue, 21 Apr 2015 12:41:15: #2 finished! INFO @ Tue, 21 Apr 2015 12:41:15: #2 predicted fragment length is 307 bps INFO @ Tue, 21 Apr 2015 12:41:15: #2 alternative fragment length(s) may be 307 bps INFO @ Tue, 21 Apr 2015 12:41:15: #2.2 Generate R script for model : SRX026742.20_model.r INFO @ Tue, 21 Apr 2015 12:41:15: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:41:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:41:16: start X-correlation... INFO @ Tue, 21 Apr 2015 12:41:16: end of X-cor INFO @ Tue, 21 Apr 2015 12:41:16: #2 finished! INFO @ Tue, 21 Apr 2015 12:41:16: #2 predicted fragment length is 307 bps INFO @ Tue, 21 Apr 2015 12:41:16: #2 alternative fragment length(s) may be 307 bps INFO @ Tue, 21 Apr 2015 12:41:16: #2.2 Generate R script for model : SRX026742.10_model.r INFO @ Tue, 21 Apr 2015 12:41:16: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:41:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:41:16: start X-correlation... INFO @ Tue, 21 Apr 2015 12:41:16: end of X-cor INFO @ Tue, 21 Apr 2015 12:41:16: #2 finished! INFO @ Tue, 21 Apr 2015 12:41:16: #2 predicted fragment length is 307 bps INFO @ Tue, 21 Apr 2015 12:41:16: #2 alternative fragment length(s) may be 307 bps INFO @ Tue, 21 Apr 2015 12:41:16: #2.2 Generate R script for model : SRX026742.05_model.r INFO @ Tue, 21 Apr 2015 12:41:16: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:41:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:41:40: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:41:40: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:41:41: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:41:59: #4 Write output xls file... SRX026742.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:41:59: #4 Write peak in narrowPeak format file... SRX026742.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:41:59: #4 Write summits bed file... SRX026742.20_summits.bed INFO @ Tue, 21 Apr 2015 12:41:59: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1563 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:42:07: #4 Write output xls file... SRX026742.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:42:07: #4 Write peak in narrowPeak format file... SRX026742.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:42:07: #4 Write summits bed file... SRX026742.10_summits.bed INFO @ Tue, 21 Apr 2015 12:42:07: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (5957 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:42:13: #4 Write output xls file... SRX026742.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:42:14: #4 Write peak in narrowPeak format file... SRX026742.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:42:14: #4 Write summits bed file... SRX026742.05_summits.bed INFO @ Tue, 21 Apr 2015 12:42:14: Done! pass1 - making usageList (13 chroms): 4 millis pass2 - checking and writing primary data (13729 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。