Job ID = 2161543 sra ファイルのダウンロード中... Completed: 395397K bytes transferred in 6 seconds (524918K bits/sec), in 3 files, 4 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 35944 0 35944 0 0 46223 0 --:--:-- --:--:-- --:--:-- 61442 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 5037444 spots for /home/okishinya/chipatlas/results/dm3/SRX027388/SRR066833.sra Written 5037444 spots total Written 5662415 spots for /home/okishinya/chipatlas/results/dm3/SRX027388/SRR066831.sra Written 5662415 spots total Written 6597770 spots for /home/okishinya/chipatlas/results/dm3/SRX027388/SRR066832.sra Written 6597770 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: 00:03:27 17297629 reads; of these: 17297629 (100.00%) were unpaired; of these: 2362718 (13.66%) aligned 0 times 13523589 (78.18%) aligned exactly 1 time 1411322 (8.16%) aligned >1 times 86.34% overall alignment rate Time searching: 00:03:27 Overall time: 00:03:27 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] 7423683 / 14934911 = 0.4971 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 12:50:46: # Command line: callpeak -t SRX027388.bam -f BAM -g dm -n SRX027388.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX027388.10 # format = BAM # ChIP-seq file = ['SRX027388.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 12:50:46: # Command line: callpeak -t SRX027388.bam -f BAM -g dm -n SRX027388.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX027388.20 # format = BAM # ChIP-seq file = ['SRX027388.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 12:50:46: # Command line: callpeak -t SRX027388.bam -f BAM -g dm -n SRX027388.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX027388.05 # format = BAM # ChIP-seq file = ['SRX027388.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 12:50:46: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:50:46: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:50:46: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:50:46: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:50:46: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:50:46: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:50:51: 1000000 INFO @ Tue, 21 Apr 2015 12:50:52: 1000000 INFO @ Tue, 21 Apr 2015 12:50:52: 1000000 INFO @ Tue, 21 Apr 2015 12:50:57: 2000000 INFO @ Tue, 21 Apr 2015 12:50:58: 2000000 INFO @ Tue, 21 Apr 2015 12:50:58: 2000000 INFO @ Tue, 21 Apr 2015 12:51:02: 3000000 INFO @ Tue, 21 Apr 2015 12:51:04: 3000000 INFO @ Tue, 21 Apr 2015 12:51:04: 3000000 INFO @ Tue, 21 Apr 2015 12:51:08: 4000000 INFO @ Tue, 21 Apr 2015 12:51:11: 4000000 INFO @ Tue, 21 Apr 2015 12:51:11: 4000000 INFO @ Tue, 21 Apr 2015 12:51:14: 5000000 INFO @ Tue, 21 Apr 2015 12:51:17: 5000000 INFO @ Tue, 21 Apr 2015 12:51:17: 5000000 INFO @ Tue, 21 Apr 2015 12:51:19: 6000000 INFO @ Tue, 21 Apr 2015 12:51:23: 6000000 INFO @ Tue, 21 Apr 2015 12:51:23: 6000000 INFO @ Tue, 21 Apr 2015 12:51:25: 7000000 INFO @ Tue, 21 Apr 2015 12:51:28: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:51:28: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:51:28: #1 total tags in treatment: 7511228 INFO @ Tue, 21 Apr 2015 12:51:28: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:51:28: #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 12:51:29: #1 tags after filtering in treatment: 7510986 INFO @ Tue, 21 Apr 2015 12:51:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:51:29: #1 finished! INFO @ Tue, 21 Apr 2015 12:51:29: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:51:30: 7000000 INFO @ Tue, 21 Apr 2015 12:51:30: 7000000 INFO @ Tue, 21 Apr 2015 12:51:31: #2 number of paired peaks: 1375 INFO @ Tue, 21 Apr 2015 12:51:31: start model_add_line... INFO @ Tue, 21 Apr 2015 12:51:33: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:51:33: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:51:33: #1 total tags in treatment: 7511228 INFO @ Tue, 21 Apr 2015 12:51:33: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:51:33: #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 12:51:33: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:51:33: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:51:33: #1 total tags in treatment: 7511228 INFO @ Tue, 21 Apr 2015 12:51:33: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:51:33: #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 12:51:34: #1 tags after filtering in treatment: 7510986 INFO @ Tue, 21 Apr 2015 12:51:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:51:34: #1 finished! INFO @ Tue, 21 Apr 2015 12:51:34: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:51:34: #1 tags after filtering in treatment: 7510986 INFO @ Tue, 21 Apr 2015 12:51:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:51:34: #1 finished! INFO @ Tue, 21 Apr 2015 12:51:34: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:51:36: #2 number of paired peaks: 1375 INFO @ Tue, 21 Apr 2015 12:51:36: start model_add_line... INFO @ Tue, 21 Apr 2015 12:51:36: #2 number of paired peaks: 1375 INFO @ Tue, 21 Apr 2015 12:51:36: start model_add_line... INFO @ Tue, 21 Apr 2015 12:51:38: start X-correlation... INFO @ Tue, 21 Apr 2015 12:51:38: end of X-cor INFO @ Tue, 21 Apr 2015 12:51:38: #2 finished! INFO @ Tue, 21 Apr 2015 12:51:38: #2 predicted fragment length is 175 bps INFO @ Tue, 21 Apr 2015 12:51:38: #2 alternative fragment length(s) may be 175 bps INFO @ Tue, 21 Apr 2015 12:51:38: #2.2 Generate R script for model : SRX027388.10_model.r INFO @ Tue, 21 Apr 2015 12:51:38: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:51:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:51:43: start X-correlation... INFO @ Tue, 21 Apr 2015 12:51:43: end of X-cor INFO @ Tue, 21 Apr 2015 12:51:43: #2 finished! INFO @ Tue, 21 Apr 2015 12:51:43: #2 predicted fragment length is 175 bps INFO @ Tue, 21 Apr 2015 12:51:43: #2 alternative fragment length(s) may be 175 bps INFO @ Tue, 21 Apr 2015 12:51:43: #2.2 Generate R script for model : SRX027388.20_model.r INFO @ Tue, 21 Apr 2015 12:51:43: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:51:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:51:43: start X-correlation... INFO @ Tue, 21 Apr 2015 12:51:43: end of X-cor INFO @ Tue, 21 Apr 2015 12:51:43: #2 finished! INFO @ Tue, 21 Apr 2015 12:51:43: #2 predicted fragment length is 175 bps INFO @ Tue, 21 Apr 2015 12:51:43: #2 alternative fragment length(s) may be 175 bps INFO @ Tue, 21 Apr 2015 12:51:43: #2.2 Generate R script for model : SRX027388.05_model.r INFO @ Tue, 21 Apr 2015 12:51:43: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:51:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:52:24: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:52:26: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:52:30: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:52:58: #4 Write output xls file... SRX027388.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:52:58: #4 Write peak in narrowPeak format file... SRX027388.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:52:58: #4 Write summits bed file... SRX027388.10_summits.bed INFO @ Tue, 21 Apr 2015 12:52:58: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2899 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:52:59: #4 Write output xls file... SRX027388.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:52:59: #4 Write peak in narrowPeak format file... SRX027388.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:52:59: #4 Write summits bed file... SRX027388.20_summits.bed INFO @ Tue, 21 Apr 2015 12:52:59: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1755 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:53:08: #4 Write output xls file... SRX027388.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:53:09: #4 Write peak in narrowPeak format file... SRX027388.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:53:09: #4 Write summits bed file... SRX027388.05_summits.bed INFO @ Tue, 21 Apr 2015 12:53:09: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4906 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。