Job ID = 2161060 sra ファイルのダウンロード中... Completed: 202503K bytes transferred in 5 seconds (301478K 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 14928 0 14928 0 0 20788 0 --:--:-- --:--:-- --:--:-- 28272 100 36055 0 36055 0 0 50141 0 --:--:-- --:--:-- --:--:-- 68285 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 8490930 spots for /home/okishinya/chipatlas/results/dm3/SRX011651/SRR027999.sra Written 8490930 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: 00:00:01 Multiseed full-index search: 00:01:32 8490930 reads; of these: 8490930 (100.00%) were unpaired; of these: 3457518 (40.72%) aligned 0 times 4246350 (50.01%) aligned exactly 1 time 787062 (9.27%) aligned >1 times 59.28% overall alignment rate Time searching: 00:01:33 Overall time: 00:01:33 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] 196062 / 5033412 = 0.0390 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 11:55:30: # Command line: callpeak -t SRX011651.bam -f BAM -g dm -n SRX011651.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX011651.05 # format = BAM # ChIP-seq file = ['SRX011651.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 11:55:30: # Command line: callpeak -t SRX011651.bam -f BAM -g dm -n SRX011651.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX011651.10 # format = BAM # ChIP-seq file = ['SRX011651.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 11:55:30: #1 read tag files... INFO @ Tue, 21 Apr 2015 11:55:30: #1 read tag files... INFO @ Tue, 21 Apr 2015 11:55:30: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 11:55:30: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 11:55:30: # Command line: callpeak -t SRX011651.bam -f BAM -g dm -n SRX011651.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX011651.20 # format = BAM # ChIP-seq file = ['SRX011651.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 11:55:30: #1 read tag files... INFO @ Tue, 21 Apr 2015 11:55:30: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 11:55:36: 1000000 INFO @ Tue, 21 Apr 2015 11:55:36: 1000000 INFO @ Tue, 21 Apr 2015 11:55:36: 1000000 INFO @ Tue, 21 Apr 2015 11:55:42: 2000000 INFO @ Tue, 21 Apr 2015 11:55:43: 2000000 INFO @ Tue, 21 Apr 2015 11:55:43: 2000000 INFO @ Tue, 21 Apr 2015 11:55:48: 3000000 INFO @ Tue, 21 Apr 2015 11:55:49: 3000000 INFO @ Tue, 21 Apr 2015 11:55:49: 3000000 INFO @ Tue, 21 Apr 2015 11:55:54: 4000000 INFO @ Tue, 21 Apr 2015 11:55:55: 4000000 INFO @ Tue, 21 Apr 2015 11:55:55: 4000000 INFO @ Tue, 21 Apr 2015 11:55:59: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 11:55:59: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 11:55:59: #1 total tags in treatment: 4837350 INFO @ Tue, 21 Apr 2015 11:55:59: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 11:55:59: #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 11:55:59: #1 tags after filtering in treatment: 4837004 INFO @ Tue, 21 Apr 2015 11:55:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 11:55:59: #1 finished! INFO @ Tue, 21 Apr 2015 11:55:59: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 11:56:00: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 11:56:00: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 11:56:00: #1 total tags in treatment: 4837350 INFO @ Tue, 21 Apr 2015 11:56:00: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 11:56:00: #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 11:56:00: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 11:56:00: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 11:56:00: #1 total tags in treatment: 4837350 INFO @ Tue, 21 Apr 2015 11:56:00: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 11:56:00: #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 11:56:00: #2 number of paired peaks: 1124 INFO @ Tue, 21 Apr 2015 11:56:00: start model_add_line... INFO @ Tue, 21 Apr 2015 11:56:01: #1 tags after filtering in treatment: 4837004 INFO @ Tue, 21 Apr 2015 11:56:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 11:56:01: #1 finished! INFO @ Tue, 21 Apr 2015 11:56:01: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 11:56:01: #1 tags after filtering in treatment: 4837004 INFO @ Tue, 21 Apr 2015 11:56:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 11:56:01: #1 finished! INFO @ Tue, 21 Apr 2015 11:56:01: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 11:56:02: #2 number of paired peaks: 1124 INFO @ Tue, 21 Apr 2015 11:56:02: start model_add_line... INFO @ Tue, 21 Apr 2015 11:56:02: #2 number of paired peaks: 1124 INFO @ Tue, 21 Apr 2015 11:56:02: start model_add_line... INFO @ Tue, 21 Apr 2015 11:56:04: start X-correlation... INFO @ Tue, 21 Apr 2015 11:56:04: end of X-cor INFO @ Tue, 21 Apr 2015 11:56:04: #2 finished! INFO @ Tue, 21 Apr 2015 11:56:04: #2 predicted fragment length is 94 bps INFO @ Tue, 21 Apr 2015 11:56:04: #2 alternative fragment length(s) may be 94 bps INFO @ Tue, 21 Apr 2015 11:56:04: #2.2 Generate R script for model : SRX011651.20_model.r INFO @ Tue, 21 Apr 2015 11:56:04: #3 Call peaks... INFO @ Tue, 21 Apr 2015 11:56:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 11:56:06: start X-correlation... INFO @ Tue, 21 Apr 2015 11:56:06: end of X-cor INFO @ Tue, 21 Apr 2015 11:56:06: #2 finished! INFO @ Tue, 21 Apr 2015 11:56:06: #2 predicted fragment length is 94 bps INFO @ Tue, 21 Apr 2015 11:56:06: #2 alternative fragment length(s) may be 94 bps INFO @ Tue, 21 Apr 2015 11:56:06: #2.2 Generate R script for model : SRX011651.05_model.r INFO @ Tue, 21 Apr 2015 11:56:06: #3 Call peaks... INFO @ Tue, 21 Apr 2015 11:56:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 11:56:06: start X-correlation... INFO @ Tue, 21 Apr 2015 11:56:06: end of X-cor INFO @ Tue, 21 Apr 2015 11:56:06: #2 finished! INFO @ Tue, 21 Apr 2015 11:56:06: #2 predicted fragment length is 94 bps INFO @ Tue, 21 Apr 2015 11:56:06: #2 alternative fragment length(s) may be 94 bps INFO @ Tue, 21 Apr 2015 11:56:06: #2.2 Generate R script for model : SRX011651.10_model.r INFO @ Tue, 21 Apr 2015 11:56:06: #3 Call peaks... INFO @ Tue, 21 Apr 2015 11:56:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 11:56:34: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 11:56:34: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 11:56:35: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 11:56:54: #4 Write output xls file... SRX011651.05_peaks.xls INFO @ Tue, 21 Apr 2015 11:56:54: #4 Write peak in narrowPeak format file... SRX011651.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 11:56:55: #4 Write summits bed file... SRX011651.05_summits.bed INFO @ Tue, 21 Apr 2015 11:56:55: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2406 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 11:56:55: #4 Write output xls file... SRX011651.20_peaks.xls INFO @ Tue, 21 Apr 2015 11:56:55: #4 Write peak in narrowPeak format file... SRX011651.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 11:56:55: #4 Write summits bed file... SRX011651.20_summits.bed INFO @ Tue, 21 Apr 2015 11:56:55: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (574 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 11:56:56: #4 Write output xls file... SRX011651.10_peaks.xls INFO @ Tue, 21 Apr 2015 11:56:56: #4 Write peak in narrowPeak format file... SRX011651.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 11:56:56: #4 Write summits bed file... SRX011651.10_summits.bed INFO @ Tue, 21 Apr 2015 11:56:56: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1250 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。