Job ID = 2161211 sra ファイルのダウンロード中... Completed: 99916K bytes transferred in 4 seconds (185965K 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 --:--:-- --:--:-- --:--:-- 0 101 5460 0 5460 0 0 10705 0 --:--:-- --:--:-- --:--:-- 17115 100 34457 0 34457 0 0 49256 0 --:--:-- --:--:-- --:--:-- 67695 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 3633782 spots for /home/okishinya/chipatlas/results/dm3/SRX013059/SRR030325.sra Written 3633782 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: 00:00:46 3633782 reads; of these: 3633782 (100.00%) were unpaired; of these: 684957 (18.85%) aligned 0 times 2608087 (71.77%) aligned exactly 1 time 340738 (9.38%) aligned >1 times 81.15% overall alignment rate Time searching: 00:00:46 Overall time: 00:00:46 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] 966980 / 2948825 = 0.3279 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 12:04:26: # Command line: callpeak -t SRX013059.bam -f BAM -g dm -n SRX013059.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013059.10 # format = BAM # ChIP-seq file = ['SRX013059.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 12:04:26: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:04:26: # Command line: callpeak -t SRX013059.bam -f BAM -g dm -n SRX013059.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013059.20 # format = BAM # ChIP-seq file = ['SRX013059.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 12:04:26: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:04:26: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:04:26: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:04:26: # Command line: callpeak -t SRX013059.bam -f BAM -g dm -n SRX013059.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013059.05 # format = BAM # ChIP-seq file = ['SRX013059.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 12:04:26: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:04:26: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:04:32: 1000000 INFO @ Tue, 21 Apr 2015 12:04:32: 1000000 INFO @ Tue, 21 Apr 2015 12:04:32: 1000000 INFO @ Tue, 21 Apr 2015 12:04:38: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:04:38: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:04:38: #1 total tags in treatment: 1981845 INFO @ Tue, 21 Apr 2015 12:04:38: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:04:38: #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 12:04:38: #1 tags after filtering in treatment: 1981745 INFO @ Tue, 21 Apr 2015 12:04:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:04:38: #1 finished! INFO @ Tue, 21 Apr 2015 12:04:38: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:04:38: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:04:38: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:04:38: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:04:38: #1 total tags in treatment: 1981845 INFO @ Tue, 21 Apr 2015 12:04:38: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:04:38: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:04:38: #1 total tags in treatment: 1981845 INFO @ Tue, 21 Apr 2015 12:04:38: #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 12:04:38: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:04:38: #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 12:04:38: #1 tags after filtering in treatment: 1981745 INFO @ Tue, 21 Apr 2015 12:04:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:04:38: #1 finished! INFO @ Tue, 21 Apr 2015 12:04:38: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:04:38: #2 number of paired peaks: 1073 INFO @ Tue, 21 Apr 2015 12:04:38: start model_add_line... INFO @ Tue, 21 Apr 2015 12:04:38: #1 tags after filtering in treatment: 1981745 INFO @ Tue, 21 Apr 2015 12:04:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:04:38: #1 finished! INFO @ Tue, 21 Apr 2015 12:04:38: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:04:39: #2 number of paired peaks: 1073 INFO @ Tue, 21 Apr 2015 12:04:39: start model_add_line... INFO @ Tue, 21 Apr 2015 12:04:39: #2 number of paired peaks: 1073 INFO @ Tue, 21 Apr 2015 12:04:39: start model_add_line... INFO @ Tue, 21 Apr 2015 12:04:40: start X-correlation... INFO @ Tue, 21 Apr 2015 12:04:40: end of X-cor INFO @ Tue, 21 Apr 2015 12:04:40: #2 finished! INFO @ Tue, 21 Apr 2015 12:04:40: #2 predicted fragment length is 110 bps INFO @ Tue, 21 Apr 2015 12:04:40: #2 alternative fragment length(s) may be 110 bps INFO @ Tue, 21 Apr 2015 12:04:40: #2.2 Generate R script for model : SRX013059.05_model.r INFO @ Tue, 21 Apr 2015 12:04:40: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:04:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:04:40: start X-correlation... INFO @ Tue, 21 Apr 2015 12:04:40: end of X-cor INFO @ Tue, 21 Apr 2015 12:04:40: #2 finished! INFO @ Tue, 21 Apr 2015 12:04:40: #2 predicted fragment length is 110 bps INFO @ Tue, 21 Apr 2015 12:04:40: #2 alternative fragment length(s) may be 110 bps INFO @ Tue, 21 Apr 2015 12:04:40: #2.2 Generate R script for model : SRX013059.10_model.r INFO @ Tue, 21 Apr 2015 12:04:40: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:04:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:04:40: start X-correlation... INFO @ Tue, 21 Apr 2015 12:04:40: end of X-cor INFO @ Tue, 21 Apr 2015 12:04:40: #2 finished! INFO @ Tue, 21 Apr 2015 12:04:40: #2 predicted fragment length is 110 bps INFO @ Tue, 21 Apr 2015 12:04:40: #2 alternative fragment length(s) may be 110 bps INFO @ Tue, 21 Apr 2015 12:04:40: #2.2 Generate R script for model : SRX013059.20_model.r INFO @ Tue, 21 Apr 2015 12:04:40: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:04:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:04:52: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:04:52: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:04:52: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:05:01: #4 Write output xls file... SRX013059.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:05:01: #4 Write peak in narrowPeak format file... SRX013059.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:05:01: #4 Write summits bed file... SRX013059.05_summits.bed INFO @ Tue, 21 Apr 2015 12:05:01: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1227 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:05:01: #4 Write output xls file... SRX013059.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:05:01: #4 Write peak in narrowPeak format file... SRX013059.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:05:01: #4 Write summits bed file... SRX013059.10_summits.bed INFO @ Tue, 21 Apr 2015 12:05:01: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (400 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:05:01: #4 Write output xls file... SRX013059.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:05:01: #4 Write peak in narrowPeak format file... SRX013059.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:05:01: #4 Write summits bed file... SRX013059.20_summits.bed INFO @ Tue, 21 Apr 2015 12:05:01: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (96 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。