Job ID = 2161228 sra ファイルのダウンロード中... Completed: 252906K bytes transferred in 5 seconds (380847K 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 34468 0 34468 0 0 48920 0 --:--:-- --:--:-- --:--:-- 67189 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 9440322 spots for /home/okishinya/chipatlas/results/dm3/SRX013076/SRR030342.sra Written 9440322 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: 00:02:16 9440322 reads; of these: 9440322 (100.00%) were unpaired; of these: 239679 (2.54%) aligned 0 times 8072676 (85.51%) aligned exactly 1 time 1127967 (11.95%) aligned >1 times 97.46% overall alignment rate Time searching: 00:02:16 Overall time: 00:02:16 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] 990962 / 9200643 = 0.1077 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 12:08:58: # Command line: callpeak -t SRX013076.bam -f BAM -g dm -n SRX013076.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013076.20 # format = BAM # ChIP-seq file = ['SRX013076.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 12:08:58: # Command line: callpeak -t SRX013076.bam -f BAM -g dm -n SRX013076.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013076.05 # format = BAM # ChIP-seq file = ['SRX013076.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 12:08:58: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:08:58: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:08:58: # Command line: callpeak -t SRX013076.bam -f BAM -g dm -n SRX013076.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013076.10 # format = BAM # ChIP-seq file = ['SRX013076.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 12:08:58: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:08:58: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:08:58: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:08:58: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:09:04: 1000000 INFO @ Tue, 21 Apr 2015 12:09:04: 1000000 INFO @ Tue, 21 Apr 2015 12:09:04: 1000000 INFO @ Tue, 21 Apr 2015 12:09:10: 2000000 INFO @ Tue, 21 Apr 2015 12:09:10: 2000000 INFO @ Tue, 21 Apr 2015 12:09:10: 2000000 INFO @ Tue, 21 Apr 2015 12:09:16: 3000000 INFO @ Tue, 21 Apr 2015 12:09:16: 3000000 INFO @ Tue, 21 Apr 2015 12:09:16: 3000000 INFO @ Tue, 21 Apr 2015 12:09:22: 4000000 INFO @ Tue, 21 Apr 2015 12:09:22: 4000000 INFO @ Tue, 21 Apr 2015 12:09:22: 4000000 INFO @ Tue, 21 Apr 2015 12:09:28: 5000000 INFO @ Tue, 21 Apr 2015 12:09:28: 5000000 INFO @ Tue, 21 Apr 2015 12:09:28: 5000000 INFO @ Tue, 21 Apr 2015 12:09:34: 6000000 INFO @ Tue, 21 Apr 2015 12:09:34: 6000000 INFO @ Tue, 21 Apr 2015 12:09:34: 6000000 INFO @ Tue, 21 Apr 2015 12:09:40: 7000000 INFO @ Tue, 21 Apr 2015 12:09:40: 7000000 INFO @ Tue, 21 Apr 2015 12:09:41: 7000000 INFO @ Tue, 21 Apr 2015 12:09:47: 8000000 INFO @ Tue, 21 Apr 2015 12:09:48: 8000000 INFO @ Tue, 21 Apr 2015 12:09:48: 8000000 INFO @ Tue, 21 Apr 2015 12:09:49: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:09:49: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:09:49: #1 total tags in treatment: 8209681 INFO @ Tue, 21 Apr 2015 12:09:49: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:09:49: #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 12:09:49: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:09:49: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:09:49: #1 total tags in treatment: 8209681 INFO @ Tue, 21 Apr 2015 12:09:49: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:09:49: #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 12:09:50: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:09:50: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:09:50: #1 total tags in treatment: 8209681 INFO @ Tue, 21 Apr 2015 12:09:50: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:09:50: #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 12:09:50: #1 tags after filtering in treatment: 8209228 INFO @ Tue, 21 Apr 2015 12:09:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:09:50: #1 finished! INFO @ Tue, 21 Apr 2015 12:09:50: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:09:50: #1 tags after filtering in treatment: 8209228 INFO @ Tue, 21 Apr 2015 12:09:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:09:50: #1 finished! INFO @ Tue, 21 Apr 2015 12:09:50: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:09:51: #1 tags after filtering in treatment: 8209228 INFO @ Tue, 21 Apr 2015 12:09:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:09:51: #1 finished! INFO @ Tue, 21 Apr 2015 12:09:51: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:09:52: #2 number of paired peaks: 1471 INFO @ Tue, 21 Apr 2015 12:09:52: start model_add_line... INFO @ Tue, 21 Apr 2015 12:09:52: #2 number of paired peaks: 1471 INFO @ Tue, 21 Apr 2015 12:09:52: start model_add_line... INFO @ Tue, 21 Apr 2015 12:09:53: #2 number of paired peaks: 1471 INFO @ Tue, 21 Apr 2015 12:09:53: start model_add_line... INFO @ Tue, 21 Apr 2015 12:09:59: start X-correlation... INFO @ Tue, 21 Apr 2015 12:09:59: end of X-cor INFO @ Tue, 21 Apr 2015 12:09:59: #2 finished! INFO @ Tue, 21 Apr 2015 12:09:59: #2 predicted fragment length is 148 bps INFO @ Tue, 21 Apr 2015 12:09:59: #2 alternative fragment length(s) may be 148 bps INFO @ Tue, 21 Apr 2015 12:09:59: #2.2 Generate R script for model : SRX013076.20_model.r INFO @ Tue, 21 Apr 2015 12:09:59: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:09:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:09:59: start X-correlation... INFO @ Tue, 21 Apr 2015 12:09:59: end of X-cor INFO @ Tue, 21 Apr 2015 12:09:59: #2 finished! INFO @ Tue, 21 Apr 2015 12:09:59: #2 predicted fragment length is 148 bps INFO @ Tue, 21 Apr 2015 12:09:59: #2 alternative fragment length(s) may be 148 bps INFO @ Tue, 21 Apr 2015 12:09:59: #2.2 Generate R script for model : SRX013076.10_model.r INFO @ Tue, 21 Apr 2015 12:09:59: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:09:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:09:59: start X-correlation... INFO @ Tue, 21 Apr 2015 12:09:59: end of X-cor INFO @ Tue, 21 Apr 2015 12:09:59: #2 finished! INFO @ Tue, 21 Apr 2015 12:09:59: #2 predicted fragment length is 148 bps INFO @ Tue, 21 Apr 2015 12:09:59: #2 alternative fragment length(s) may be 148 bps INFO @ Tue, 21 Apr 2015 12:09:59: #2.2 Generate R script for model : SRX013076.05_model.r INFO @ Tue, 21 Apr 2015 12:09:59: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:09:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:10:46: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:10:47: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:10:48: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:11:22: #4 Write output xls file... SRX013076.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:11:22: #4 Write peak in narrowPeak format file... SRX013076.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:11:22: #4 Write summits bed file... SRX013076.20_summits.bed INFO @ Tue, 21 Apr 2015 12:11:22: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1050 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:11:25: #4 Write output xls file... SRX013076.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:11:25: #4 Write peak in narrowPeak format file... SRX013076.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:11:25: #4 Write summits bed file... SRX013076.10_summits.bed INFO @ Tue, 21 Apr 2015 12:11:25: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (4491 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:11:30: #4 Write output xls file... SRX013076.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:11:30: #4 Write peak in narrowPeak format file... SRX013076.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:11:30: #4 Write summits bed file... SRX013076.05_summits.bed INFO @ Tue, 21 Apr 2015 12:11:30: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (9412 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。