Job ID = 2161071 sra ファイルのダウンロード中... Completed: 122814K bytes transferred in 4 seconds (207787K 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 10635 0 --:--:-- --:--:-- --:--:-- 16904 100 34541 0 34541 0 0 49121 0 --:--:-- --:--:-- --:--:-- 67331 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 5172679 spots for /home/okishinya/chipatlas/results/dm3/SRX013007/SRR030273.sra Written 5172679 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: 00:01:08 5172679 reads; of these: 5172679 (100.00%) were unpaired; of these: 815511 (15.77%) aligned 0 times 3831551 (74.07%) aligned exactly 1 time 525617 (10.16%) aligned >1 times 84.23% overall alignment rate Time searching: 00:01:08 Overall time: 00:01:08 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] 377458 / 4357168 = 0.0866 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 11:55:14: # Command line: callpeak -t SRX013007.bam -f BAM -g dm -n SRX013007.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013007.20 # format = BAM # ChIP-seq file = ['SRX013007.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 11:55:14: # Command line: callpeak -t SRX013007.bam -f BAM -g dm -n SRX013007.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013007.10 # format = BAM # ChIP-seq file = ['SRX013007.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 11:55:14: #1 read tag files... INFO @ Tue, 21 Apr 2015 11:55:14: # Command line: callpeak -t SRX013007.bam -f BAM -g dm -n SRX013007.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013007.05 # format = BAM # ChIP-seq file = ['SRX013007.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 11:55:14: #1 read tag files... INFO @ Tue, 21 Apr 2015 11:55:14: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 11:55:14: #1 read tag files... INFO @ Tue, 21 Apr 2015 11:55:14: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 11:55:14: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 11:55:19: 1000000 INFO @ Tue, 21 Apr 2015 11:55:19: 1000000 INFO @ Tue, 21 Apr 2015 11:55:19: 1000000 INFO @ Tue, 21 Apr 2015 11:55:24: 2000000 INFO @ Tue, 21 Apr 2015 11:55:24: 2000000 INFO @ Tue, 21 Apr 2015 11:55:24: 2000000 INFO @ Tue, 21 Apr 2015 11:55:29: 3000000 INFO @ Tue, 21 Apr 2015 11:55:29: 3000000 INFO @ Tue, 21 Apr 2015 11:55:29: 3000000 INFO @ Tue, 21 Apr 2015 11:55:34: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 11:55:34: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 11:55:34: #1 total tags in treatment: 3979710 INFO @ Tue, 21 Apr 2015 11:55:34: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 11:55:34: #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 11:55:34: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 11:55:34: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 11:55:34: #1 total tags in treatment: 3979710 INFO @ Tue, 21 Apr 2015 11:55:34: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 11:55:34: #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 11:55:34: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 11:55:34: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 11:55:34: #1 total tags in treatment: 3979710 INFO @ Tue, 21 Apr 2015 11:55:34: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 11:55:34: #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 11:55:35: #1 tags after filtering in treatment: 3979237 INFO @ Tue, 21 Apr 2015 11:55:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 11:55:35: #1 finished! INFO @ Tue, 21 Apr 2015 11:55:35: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 11:55:35: #1 tags after filtering in treatment: 3979237 INFO @ Tue, 21 Apr 2015 11:55:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 11:55:35: #1 finished! INFO @ Tue, 21 Apr 2015 11:55:35: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 11:55:35: #1 tags after filtering in treatment: 3979237 INFO @ Tue, 21 Apr 2015 11:55:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 11:55:35: #1 finished! INFO @ Tue, 21 Apr 2015 11:55:35: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 11:55:36: #2 number of paired peaks: 3696 INFO @ Tue, 21 Apr 2015 11:55:36: start model_add_line... INFO @ Tue, 21 Apr 2015 11:55:36: #2 number of paired peaks: 3696 INFO @ Tue, 21 Apr 2015 11:55:36: start model_add_line... INFO @ Tue, 21 Apr 2015 11:55:36: #2 number of paired peaks: 3696 INFO @ Tue, 21 Apr 2015 11:55:36: start model_add_line... INFO @ Tue, 21 Apr 2015 11:55:44: start X-correlation... INFO @ Tue, 21 Apr 2015 11:55:44: end of X-cor INFO @ Tue, 21 Apr 2015 11:55:44: #2 finished! INFO @ Tue, 21 Apr 2015 11:55:44: #2 predicted fragment length is 177 bps INFO @ Tue, 21 Apr 2015 11:55:44: #2 alternative fragment length(s) may be 177 bps INFO @ Tue, 21 Apr 2015 11:55:44: #2.2 Generate R script for model : SRX013007.05_model.r INFO @ Tue, 21 Apr 2015 11:55:44: #3 Call peaks... INFO @ Tue, 21 Apr 2015 11:55:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 11:55:44: start X-correlation... INFO @ Tue, 21 Apr 2015 11:55:44: end of X-cor INFO @ Tue, 21 Apr 2015 11:55:44: #2 finished! INFO @ Tue, 21 Apr 2015 11:55:44: #2 predicted fragment length is 177 bps INFO @ Tue, 21 Apr 2015 11:55:44: #2 alternative fragment length(s) may be 177 bps INFO @ Tue, 21 Apr 2015 11:55:44: #2.2 Generate R script for model : SRX013007.20_model.r INFO @ Tue, 21 Apr 2015 11:55:44: #3 Call peaks... INFO @ Tue, 21 Apr 2015 11:55:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 11:55:44: start X-correlation... INFO @ Tue, 21 Apr 2015 11:55:44: end of X-cor INFO @ Tue, 21 Apr 2015 11:55:44: #2 finished! INFO @ Tue, 21 Apr 2015 11:55:44: #2 predicted fragment length is 177 bps INFO @ Tue, 21 Apr 2015 11:55:44: #2 alternative fragment length(s) may be 177 bps INFO @ Tue, 21 Apr 2015 11:55:44: #2.2 Generate R script for model : SRX013007.10_model.r INFO @ Tue, 21 Apr 2015 11:55:44: #3 Call peaks... INFO @ Tue, 21 Apr 2015 11:55:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 11:56:07: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 11:56:07: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 11:56:08: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 11:56:25: #4 Write output xls file... SRX013007.20_peaks.xls INFO @ Tue, 21 Apr 2015 11:56:25: #4 Write peak in narrowPeak format file... SRX013007.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 11:56:25: #4 Write summits bed file... SRX013007.20_summits.bed INFO @ Tue, 21 Apr 2015 11:56:25: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (731 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 11:56:27: #4 Write output xls file... SRX013007.10_peaks.xls INFO @ Tue, 21 Apr 2015 11:56:27: #4 Write peak in narrowPeak format file... SRX013007.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 11:56:27: #4 Write summits bed file... SRX013007.10_summits.bed INFO @ Tue, 21 Apr 2015 11:56:27: Done! pass1 - making usageList (10 chroms): 2 millis pass2 - checking and writing primary data (2972 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 11:56:29: #4 Write output xls file... SRX013007.05_peaks.xls INFO @ Tue, 21 Apr 2015 11:56:29: #4 Write peak in narrowPeak format file... SRX013007.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 11:56:30: #4 Write summits bed file... SRX013007.05_summits.bed INFO @ Tue, 21 Apr 2015 11:56:30: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (5436 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。