Job ID = 2161087 sra ファイルのダウンロード中... Completed: 82441K bytes transferred in 4 seconds (161276K 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 34519 0 34519 0 0 51455 0 --:--:-- --:--:-- --:--:-- 72064 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 4045663 spots for /home/okishinya/chipatlas/results/dm3/SRX013017/SRR030283.sra Written 4045663 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: 00:00:48 4045663 reads; of these: 4045663 (100.00%) were unpaired; of these: 196648 (4.86%) aligned 0 times 3592492 (88.80%) aligned exactly 1 time 256523 (6.34%) aligned >1 times 95.14% overall alignment rate Time searching: 00:00:48 Overall time: 00:00:48 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] 370494 / 3849015 = 0.0963 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 11:57:00: # Command line: callpeak -t SRX013017.bam -f BAM -g dm -n SRX013017.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013017.20 # format = BAM # ChIP-seq file = ['SRX013017.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 11:57:00: #1 read tag files... INFO @ Tue, 21 Apr 2015 11:57:00: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 11:57:00: # Command line: callpeak -t SRX013017.bam -f BAM -g dm -n SRX013017.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013017.10 # format = BAM # ChIP-seq file = ['SRX013017.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 11:57:00: # Command line: callpeak -t SRX013017.bam -f BAM -g dm -n SRX013017.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013017.05 # format = BAM # ChIP-seq file = ['SRX013017.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 11:57:00: #1 read tag files... INFO @ Tue, 21 Apr 2015 11:57:00: #1 read tag files... INFO @ Tue, 21 Apr 2015 11:57:00: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 11:57:00: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 11:57:05: 1000000 INFO @ Tue, 21 Apr 2015 11:57:05: 1000000 INFO @ Tue, 21 Apr 2015 11:57:05: 1000000 INFO @ Tue, 21 Apr 2015 11:57:10: 2000000 INFO @ Tue, 21 Apr 2015 11:57:10: 2000000 INFO @ Tue, 21 Apr 2015 11:57:11: 2000000 INFO @ Tue, 21 Apr 2015 11:57:15: 3000000 INFO @ Tue, 21 Apr 2015 11:57:16: 3000000 INFO @ Tue, 21 Apr 2015 11:57:16: 3000000 INFO @ Tue, 21 Apr 2015 11:57:17: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 11:57:17: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 11:57:17: #1 total tags in treatment: 3478521 INFO @ Tue, 21 Apr 2015 11:57:17: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 11:57:17: #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 11:57:18: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 11:57:18: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 11:57:18: #1 total tags in treatment: 3478521 INFO @ Tue, 21 Apr 2015 11:57:18: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 11:57:18: #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 11:57:18: #1 tags after filtering in treatment: 3478391 INFO @ Tue, 21 Apr 2015 11:57:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 11:57:18: #1 finished! INFO @ Tue, 21 Apr 2015 11:57:18: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 11:57:18: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 11:57:18: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 11:57:18: #1 total tags in treatment: 3478521 INFO @ Tue, 21 Apr 2015 11:57:18: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 11:57:18: #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 11:57:19: #1 tags after filtering in treatment: 3478391 INFO @ Tue, 21 Apr 2015 11:57:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 11:57:19: #1 finished! INFO @ Tue, 21 Apr 2015 11:57:19: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 11:57:19: #1 tags after filtering in treatment: 3478391 INFO @ Tue, 21 Apr 2015 11:57:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 11:57:19: #1 finished! INFO @ Tue, 21 Apr 2015 11:57:19: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 11:57:20: #2 number of paired peaks: 8471 INFO @ Tue, 21 Apr 2015 11:57:20: start model_add_line... INFO @ Tue, 21 Apr 2015 11:57:20: #2 number of paired peaks: 8471 INFO @ Tue, 21 Apr 2015 11:57:20: start model_add_line... INFO @ Tue, 21 Apr 2015 11:57:21: #2 number of paired peaks: 8471 INFO @ Tue, 21 Apr 2015 11:57:21: start model_add_line... INFO @ Tue, 21 Apr 2015 11:57:44: start X-correlation... INFO @ Tue, 21 Apr 2015 11:57:44: end of X-cor INFO @ Tue, 21 Apr 2015 11:57:44: #2 finished! INFO @ Tue, 21 Apr 2015 11:57:44: #2 predicted fragment length is 169 bps INFO @ Tue, 21 Apr 2015 11:57:44: #2 alternative fragment length(s) may be 169 bps INFO @ Tue, 21 Apr 2015 11:57:44: #2.2 Generate R script for model : SRX013017.20_model.r INFO @ Tue, 21 Apr 2015 11:57:44: #3 Call peaks... INFO @ Tue, 21 Apr 2015 11:57:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 11:57:45: start X-correlation... INFO @ Tue, 21 Apr 2015 11:57:45: end of X-cor INFO @ Tue, 21 Apr 2015 11:57:45: #2 finished! INFO @ Tue, 21 Apr 2015 11:57:45: #2 predicted fragment length is 169 bps INFO @ Tue, 21 Apr 2015 11:57:45: #2 alternative fragment length(s) may be 169 bps INFO @ Tue, 21 Apr 2015 11:57:45: #2.2 Generate R script for model : SRX013017.05_model.r INFO @ Tue, 21 Apr 2015 11:57:45: #3 Call peaks... INFO @ Tue, 21 Apr 2015 11:57:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 11:57:45: start X-correlation... INFO @ Tue, 21 Apr 2015 11:57:45: end of X-cor INFO @ Tue, 21 Apr 2015 11:57:45: #2 finished! INFO @ Tue, 21 Apr 2015 11:57:45: #2 predicted fragment length is 169 bps INFO @ Tue, 21 Apr 2015 11:57:45: #2 alternative fragment length(s) may be 169 bps INFO @ Tue, 21 Apr 2015 11:57:45: #2.2 Generate R script for model : SRX013017.10_model.r INFO @ Tue, 21 Apr 2015 11:57:45: #3 Call peaks... INFO @ Tue, 21 Apr 2015 11:57:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 11:58:05: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 11:58:05: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 11:58:06: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 21 Apr 2015 11:58:24: #4 Write output xls file... SRX013017.20_peaks.xls INFO @ Tue, 21 Apr 2015 11:58:24: #4 Write peak in narrowPeak format file... SRX013017.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 11:58:24: #4 Write summits bed file... SRX013017.20_summits.bed INFO @ Tue, 21 Apr 2015 11:58:24: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3434 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 11:58:26: #4 Write output xls file... SRX013017.10_peaks.xls INFO @ Tue, 21 Apr 2015 11:58:26: #4 Write peak in narrowPeak format file... SRX013017.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 11:58:26: #4 Write summits bed file... SRX013017.10_summits.bed INFO @ Tue, 21 Apr 2015 11:58:26: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (5165 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 11:58:28: #4 Write output xls file... SRX013017.05_peaks.xls INFO @ Tue, 21 Apr 2015 11:58:28: #4 Write peak in narrowPeak format file... SRX013017.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 11:58:28: #4 Write summits bed file... SRX013017.05_summits.bed INFO @ Tue, 21 Apr 2015 11:58:28: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6345 records, 4 fields): 10 millis CompletedMACS2peakCalling