Job ID = 2161348 sra ファイルのダウンロード中... Completed: 859025K bytes transferred in 9 seconds (723295K bits/sec), in 2 files, 3 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 35404 0 35404 0 0 48103 0 --:--:-- --:--:-- --:--:-- 65080 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 10207389 spots for /home/okishinya/chipatlas/results/dm3/SRX020697/SRR060776.sra Written 10207389 spots total Written 18869507 spots for /home/okishinya/chipatlas/results/dm3/SRX020697/SRR060775.sra Written 18869507 spots total 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: 00:05:30 29076896 reads; of these: 29076896 (100.00%) were unpaired; of these: 14836136 (51.02%) aligned 0 times 11300252 (38.86%) aligned exactly 1 time 2940508 (10.11%) aligned >1 times 48.98% overall alignment rate Time searching: 00:05:30 Overall time: 00:05:30 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] 2931925 / 14240760 = 0.2059 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 12:35:25: # Command line: callpeak -t SRX020697.bam -f BAM -g dm -n SRX020697.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX020697.05 # format = BAM # ChIP-seq file = ['SRX020697.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 12:35:25: # Command line: callpeak -t SRX020697.bam -f BAM -g dm -n SRX020697.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX020697.10 # format = BAM # ChIP-seq file = ['SRX020697.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 12:35:25: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:35:25: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:35:25: # Command line: callpeak -t SRX020697.bam -f BAM -g dm -n SRX020697.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX020697.20 # format = BAM # ChIP-seq file = ['SRX020697.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 12:35:25: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:35:25: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:35:25: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:35:25: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:35:31: 1000000 INFO @ Tue, 21 Apr 2015 12:35:31: 1000000 INFO @ Tue, 21 Apr 2015 12:35:31: 1000000 INFO @ Tue, 21 Apr 2015 12:35:37: 2000000 INFO @ Tue, 21 Apr 2015 12:35:37: 2000000 INFO @ Tue, 21 Apr 2015 12:35:37: 2000000 INFO @ Tue, 21 Apr 2015 12:35:43: 3000000 INFO @ Tue, 21 Apr 2015 12:35:44: 3000000 INFO @ Tue, 21 Apr 2015 12:35:44: 3000000 INFO @ Tue, 21 Apr 2015 12:35:49: 4000000 INFO @ Tue, 21 Apr 2015 12:35:50: 4000000 INFO @ Tue, 21 Apr 2015 12:35:50: 4000000 INFO @ Tue, 21 Apr 2015 12:35:56: 5000000 INFO @ Tue, 21 Apr 2015 12:35:57: 5000000 INFO @ Tue, 21 Apr 2015 12:35:57: 5000000 INFO @ Tue, 21 Apr 2015 12:36:02: 6000000 INFO @ Tue, 21 Apr 2015 12:36:03: 6000000 INFO @ Tue, 21 Apr 2015 12:36:03: 6000000 INFO @ Tue, 21 Apr 2015 12:36:08: 7000000 INFO @ Tue, 21 Apr 2015 12:36:09: 7000000 INFO @ Tue, 21 Apr 2015 12:36:09: 7000000 INFO @ Tue, 21 Apr 2015 12:36:14: 8000000 INFO @ Tue, 21 Apr 2015 12:36:16: 8000000 INFO @ Tue, 21 Apr 2015 12:36:16: 8000000 INFO @ Tue, 21 Apr 2015 12:36:21: 9000000 INFO @ Tue, 21 Apr 2015 12:36:22: 9000000 INFO @ Tue, 21 Apr 2015 12:36:22: 9000000 INFO @ Tue, 21 Apr 2015 12:36:27: 10000000 INFO @ Tue, 21 Apr 2015 12:36:28: 10000000 INFO @ Tue, 21 Apr 2015 12:36:28: 10000000 INFO @ Tue, 21 Apr 2015 12:36:33: 11000000 INFO @ Tue, 21 Apr 2015 12:36:35: 11000000 INFO @ Tue, 21 Apr 2015 12:36:35: 11000000 INFO @ Tue, 21 Apr 2015 12:36:35: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:36:35: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:36:35: #1 total tags in treatment: 11308835 INFO @ Tue, 21 Apr 2015 12:36:35: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:36:35: #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 12:36:37: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:36:37: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:36:37: #1 total tags in treatment: 11308835 INFO @ Tue, 21 Apr 2015 12:36:37: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:36:37: #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 12:36:37: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:36:37: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:36:37: #1 total tags in treatment: 11308835 INFO @ Tue, 21 Apr 2015 12:36:37: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:36:37: #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 12:36:37: #1 tags after filtering in treatment: 11305958 INFO @ Tue, 21 Apr 2015 12:36:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:36:37: #1 finished! INFO @ Tue, 21 Apr 2015 12:36:37: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:36:39: #1 tags after filtering in treatment: 11305958 INFO @ Tue, 21 Apr 2015 12:36:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:36:39: #1 finished! INFO @ Tue, 21 Apr 2015 12:36:39: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:36:39: #1 tags after filtering in treatment: 11305958 INFO @ Tue, 21 Apr 2015 12:36:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:36:39: #1 finished! INFO @ Tue, 21 Apr 2015 12:36:39: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:36:40: #2 number of paired peaks: 1176 INFO @ Tue, 21 Apr 2015 12:36:40: start model_add_line... INFO @ Tue, 21 Apr 2015 12:36:41: #2 number of paired peaks: 1176 INFO @ Tue, 21 Apr 2015 12:36:41: start model_add_line... INFO @ Tue, 21 Apr 2015 12:36:41: #2 number of paired peaks: 1176 INFO @ Tue, 21 Apr 2015 12:36:41: start model_add_line... INFO @ Tue, 21 Apr 2015 12:36:48: start X-correlation... INFO @ Tue, 21 Apr 2015 12:36:48: end of X-cor INFO @ Tue, 21 Apr 2015 12:36:48: #2 finished! INFO @ Tue, 21 Apr 2015 12:36:48: #2 predicted fragment length is 75 bps INFO @ Tue, 21 Apr 2015 12:36:48: #2 alternative fragment length(s) may be 75 bps INFO @ Tue, 21 Apr 2015 12:36:48: #2.2 Generate R script for model : SRX020697.20_model.r INFO @ Tue, 21 Apr 2015 12:36:48: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:36:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:36:49: start X-correlation... INFO @ Tue, 21 Apr 2015 12:36:49: end of X-cor INFO @ Tue, 21 Apr 2015 12:36:49: #2 finished! INFO @ Tue, 21 Apr 2015 12:36:49: #2 predicted fragment length is 75 bps INFO @ Tue, 21 Apr 2015 12:36:49: #2 alternative fragment length(s) may be 75 bps INFO @ Tue, 21 Apr 2015 12:36:49: #2.2 Generate R script for model : SRX020697.05_model.r INFO @ Tue, 21 Apr 2015 12:36:49: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:36:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:36:50: start X-correlation... INFO @ Tue, 21 Apr 2015 12:36:50: end of X-cor INFO @ Tue, 21 Apr 2015 12:36:50: #2 finished! INFO @ Tue, 21 Apr 2015 12:36:50: #2 predicted fragment length is 75 bps INFO @ Tue, 21 Apr 2015 12:36:50: #2 alternative fragment length(s) may be 75 bps INFO @ Tue, 21 Apr 2015 12:36:50: #2.2 Generate R script for model : SRX020697.10_model.r INFO @ Tue, 21 Apr 2015 12:36:50: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:36:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:37:46: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:37:49: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:37:50: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:38:31: #4 Write output xls file... SRX020697.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:38:31: #4 Write peak in narrowPeak format file... SRX020697.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:38:31: #4 Write summits bed file... SRX020697.20_summits.bed INFO @ Tue, 21 Apr 2015 12:38:31: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1942 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:38:35: #4 Write output xls file... SRX020697.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:38:35: #4 Write peak in narrowPeak format file... SRX020697.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:38:35: #4 Write summits bed file... SRX020697.10_summits.bed INFO @ Tue, 21 Apr 2015 12:38:35: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5899 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:38:43: #4 Write output xls file... SRX020697.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:38:43: #4 Write peak in narrowPeak format file... SRX020697.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:38:43: #4 Write summits bed file... SRX020697.05_summits.bed INFO @ Tue, 21 Apr 2015 12:38:43: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (11097 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。