Job ID = 2162393 sra ファイルのダウンロード中... Completed: 511702K bytes transferred in 8 seconds (476425K 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 37935 0 37935 0 0 47522 0 --:--:-- --:--:-- --:--:-- 62495 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 24960633 spots for /home/okishinya/chipatlas/results/dm3/SRX084383/SRR314829.sra Written 24960633 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: 00:06:35 24960633 reads; of these: 24960633 (100.00%) were unpaired; of these: 6048678 (24.23%) aligned 0 times 13542489 (54.26%) aligned exactly 1 time 5369466 (21.51%) aligned >1 times 75.77% overall alignment rate Time searching: 00:06:35 Overall time: 00:06:35 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_sort_core] merging from 8 files... [bam_rmdupse_core] 12787100 / 18911955 = 0.6761 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 13:53:35: # Command line: callpeak -t SRX084383.bam -f BAM -g dm -n SRX084383.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX084383.10 # format = BAM # ChIP-seq file = ['SRX084383.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 13:53:35: # Command line: callpeak -t SRX084383.bam -f BAM -g dm -n SRX084383.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX084383.05 # format = BAM # ChIP-seq file = ['SRX084383.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 13:53:35: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:53:35: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:53:35: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:53:35: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:53:35: # Command line: callpeak -t SRX084383.bam -f BAM -g dm -n SRX084383.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX084383.20 # format = BAM # ChIP-seq file = ['SRX084383.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 13:53:35: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:53:35: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:53:40: 1000000 INFO @ Tue, 21 Apr 2015 13:53:40: 1000000 INFO @ Tue, 21 Apr 2015 13:53:40: 1000000 INFO @ Tue, 21 Apr 2015 13:53:45: 2000000 INFO @ Tue, 21 Apr 2015 13:53:45: 2000000 INFO @ Tue, 21 Apr 2015 13:53:45: 2000000 INFO @ Tue, 21 Apr 2015 13:53:50: 3000000 INFO @ Tue, 21 Apr 2015 13:53:50: 3000000 INFO @ Tue, 21 Apr 2015 13:53:50: 3000000 INFO @ Tue, 21 Apr 2015 13:53:55: 4000000 INFO @ Tue, 21 Apr 2015 13:53:55: 4000000 INFO @ Tue, 21 Apr 2015 13:53:55: 4000000 INFO @ Tue, 21 Apr 2015 13:53:59: 5000000 INFO @ Tue, 21 Apr 2015 13:54:01: 5000000 INFO @ Tue, 21 Apr 2015 13:54:01: 5000000 INFO @ Tue, 21 Apr 2015 13:54:04: 6000000 INFO @ Tue, 21 Apr 2015 13:54:05: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 13:54:05: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 13:54:05: #1 total tags in treatment: 6124855 INFO @ Tue, 21 Apr 2015 13:54:05: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:54:05: #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 13:54:06: 6000000 INFO @ Tue, 21 Apr 2015 13:54:06: 6000000 INFO @ Tue, 21 Apr 2015 13:54:06: #1 tags after filtering in treatment: 6122669 INFO @ Tue, 21 Apr 2015 13:54:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:54:06: #1 finished! INFO @ Tue, 21 Apr 2015 13:54:06: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:54:07: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 13:54:07: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 13:54:07: #1 total tags in treatment: 6124855 INFO @ Tue, 21 Apr 2015 13:54:07: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:54:07: #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 13:54:07: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 13:54:07: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 13:54:07: #1 total tags in treatment: 6124855 INFO @ Tue, 21 Apr 2015 13:54:07: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:54:07: #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 13:54:08: #1 tags after filtering in treatment: 6122669 INFO @ Tue, 21 Apr 2015 13:54:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:54:08: #1 finished! INFO @ Tue, 21 Apr 2015 13:54:08: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:54:08: #1 tags after filtering in treatment: 6122669 INFO @ Tue, 21 Apr 2015 13:54:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:54:08: #1 finished! INFO @ Tue, 21 Apr 2015 13:54:08: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:54:08: #2 number of paired peaks: 4810 INFO @ Tue, 21 Apr 2015 13:54:08: start model_add_line... INFO @ Tue, 21 Apr 2015 13:54:09: #2 number of paired peaks: 4810 INFO @ Tue, 21 Apr 2015 13:54:09: start model_add_line... INFO @ Tue, 21 Apr 2015 13:54:10: #2 number of paired peaks: 4810 INFO @ Tue, 21 Apr 2015 13:54:10: start model_add_line... INFO @ Tue, 21 Apr 2015 13:54:30: start X-correlation... INFO @ Tue, 21 Apr 2015 13:54:30: end of X-cor INFO @ Tue, 21 Apr 2015 13:54:30: #2 finished! INFO @ Tue, 21 Apr 2015 13:54:30: #2 predicted fragment length is 140 bps INFO @ Tue, 21 Apr 2015 13:54:30: #2 alternative fragment length(s) may be 140 bps INFO @ Tue, 21 Apr 2015 13:54:30: #2.2 Generate R script for model : SRX084383.20_model.r INFO @ Tue, 21 Apr 2015 13:54:30: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:54:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:54:33: start X-correlation... INFO @ Tue, 21 Apr 2015 13:54:33: end of X-cor INFO @ Tue, 21 Apr 2015 13:54:33: #2 finished! INFO @ Tue, 21 Apr 2015 13:54:33: #2 predicted fragment length is 140 bps INFO @ Tue, 21 Apr 2015 13:54:33: #2 alternative fragment length(s) may be 140 bps INFO @ Tue, 21 Apr 2015 13:54:33: #2.2 Generate R script for model : SRX084383.10_model.r INFO @ Tue, 21 Apr 2015 13:54:33: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:54:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:54:33: start X-correlation... INFO @ Tue, 21 Apr 2015 13:54:33: end of X-cor INFO @ Tue, 21 Apr 2015 13:54:33: #2 finished! INFO @ Tue, 21 Apr 2015 13:54:33: #2 predicted fragment length is 140 bps INFO @ Tue, 21 Apr 2015 13:54:33: #2 alternative fragment length(s) may be 140 bps INFO @ Tue, 21 Apr 2015 13:54:33: #2.2 Generate R script for model : SRX084383.05_model.r INFO @ Tue, 21 Apr 2015 13:54:33: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:54:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:55:08: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:55:10: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:55:10: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 21 Apr 2015 13:55:39: #4 Write output xls file... SRX084383.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:55:39: #4 Write peak in narrowPeak format file... SRX084383.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:55:39: #4 Write summits bed file... SRX084383.20_summits.bed INFO @ Tue, 21 Apr 2015 13:55:39: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (6097 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:55:45: #4 Write output xls file... SRX084383.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:55:45: #4 Write peak in narrowPeak format file... SRX084383.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:55:45: #4 Write summits bed file... SRX084383.10_summits.bed INFO @ Tue, 21 Apr 2015 13:55:45: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9361 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:55:50: #4 Write output xls file... SRX084383.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:55:50: #4 Write peak in narrowPeak format file... SRX084383.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:55:50: #4 Write summits bed file... SRX084383.05_summits.bed INFO @ Tue, 21 Apr 2015 13:55:50: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (13312 records, 4 fields): 17 millis CompletedMACS2peakCalling BigWig に変換しました。