Job ID = 2161254 sra ファイルのダウンロード中... Completed: 78051K bytes transferred in 4 seconds (149907K 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 15658 0 15658 0 0 22515 0 --:--:-- --:--:-- --:--:-- 31005 100 34739 0 34739 0 0 49893 0 --:--:-- --:--:-- --:--:-- 68654 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 3283838 spots for /home/okishinya/chipatlas/results/dm3/SRX013098/SRR030364.sra Written 3283838 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: 00:01:21 3283838 reads; of these: 3283838 (100.00%) were unpaired; of these: 437556 (13.32%) aligned 0 times 1382221 (42.09%) aligned exactly 1 time 1464061 (44.58%) aligned >1 times 86.68% overall alignment rate Time searching: 00:01:21 Overall time: 00:01:21 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] 266958 / 2846282 = 0.0938 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 12:09:49: # Command line: callpeak -t SRX013098.bam -f BAM -g dm -n SRX013098.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013098.20 # format = BAM # ChIP-seq file = ['SRX013098.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 12:09:49: # Command line: callpeak -t SRX013098.bam -f BAM -g dm -n SRX013098.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013098.05 # format = BAM # ChIP-seq file = ['SRX013098.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 12:09:49: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:09:49: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:09:49: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:09:49: # Command line: callpeak -t SRX013098.bam -f BAM -g dm -n SRX013098.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013098.10 # format = BAM # ChIP-seq file = ['SRX013098.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 12:09:49: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:09:49: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:09:49: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:09:55: 1000000 INFO @ Tue, 21 Apr 2015 12:09:56: 1000000 INFO @ Tue, 21 Apr 2015 12:09:56: 1000000 INFO @ Tue, 21 Apr 2015 12:10:00: 2000000 INFO @ Tue, 21 Apr 2015 12:10:02: 2000000 INFO @ Tue, 21 Apr 2015 12:10:02: 2000000 INFO @ Tue, 21 Apr 2015 12:10:04: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:10:04: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:10:04: #1 total tags in treatment: 2579324 INFO @ Tue, 21 Apr 2015 12:10:04: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:10:04: #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 12:10:04: #1 tags after filtering in treatment: 2578895 INFO @ Tue, 21 Apr 2015 12:10:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:10:04: #1 finished! INFO @ Tue, 21 Apr 2015 12:10:04: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:10:05: #2 number of paired peaks: 1235 INFO @ Tue, 21 Apr 2015 12:10:05: start model_add_line... INFO @ Tue, 21 Apr 2015 12:10:05: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:10:05: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:10:05: #1 total tags in treatment: 2579324 INFO @ Tue, 21 Apr 2015 12:10:05: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:10:05: #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 12:10:05: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:10:05: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:10:05: #1 total tags in treatment: 2579324 INFO @ Tue, 21 Apr 2015 12:10:05: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:10:05: #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 12:10:06: #1 tags after filtering in treatment: 2578895 INFO @ Tue, 21 Apr 2015 12:10:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:10:06: #1 finished! INFO @ Tue, 21 Apr 2015 12:10:06: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:10:06: #1 tags after filtering in treatment: 2578895 INFO @ Tue, 21 Apr 2015 12:10:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:10:06: #1 finished! INFO @ Tue, 21 Apr 2015 12:10:06: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:10:06: #2 number of paired peaks: 1235 INFO @ Tue, 21 Apr 2015 12:10:06: start model_add_line... INFO @ Tue, 21 Apr 2015 12:10:06: #2 number of paired peaks: 1235 INFO @ Tue, 21 Apr 2015 12:10:06: start model_add_line... INFO @ Tue, 21 Apr 2015 12:10:07: start X-correlation... INFO @ Tue, 21 Apr 2015 12:10:07: end of X-cor INFO @ Tue, 21 Apr 2015 12:10:07: #2 finished! INFO @ Tue, 21 Apr 2015 12:10:07: #2 predicted fragment length is 98 bps INFO @ Tue, 21 Apr 2015 12:10:07: #2 alternative fragment length(s) may be 98 bps INFO @ Tue, 21 Apr 2015 12:10:07: #2.2 Generate R script for model : SRX013098.10_model.r INFO @ Tue, 21 Apr 2015 12:10:07: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:10:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:10:08: start X-correlation... INFO @ Tue, 21 Apr 2015 12:10:08: end of X-cor INFO @ Tue, 21 Apr 2015 12:10:08: #2 finished! INFO @ Tue, 21 Apr 2015 12:10:08: #2 predicted fragment length is 98 bps INFO @ Tue, 21 Apr 2015 12:10:08: #2 alternative fragment length(s) may be 98 bps INFO @ Tue, 21 Apr 2015 12:10:08: #2.2 Generate R script for model : SRX013098.05_model.r INFO @ Tue, 21 Apr 2015 12:10:08: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:10:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:10:08: start X-correlation... INFO @ Tue, 21 Apr 2015 12:10:08: end of X-cor INFO @ Tue, 21 Apr 2015 12:10:08: #2 finished! INFO @ Tue, 21 Apr 2015 12:10:08: #2 predicted fragment length is 98 bps INFO @ Tue, 21 Apr 2015 12:10:08: #2 alternative fragment length(s) may be 98 bps INFO @ Tue, 21 Apr 2015 12:10:08: #2.2 Generate R script for model : SRX013098.20_model.r INFO @ Tue, 21 Apr 2015 12:10:08: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:10:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:10:22: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:10:23: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:10:24: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:10:33: #4 Write output xls file... SRX013098.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:10:33: #4 Write peak in narrowPeak format file... SRX013098.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:10:33: #4 Write summits bed file... SRX013098.10_summits.bed INFO @ Tue, 21 Apr 2015 12:10:33: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (686 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:10:35: #4 Write output xls file... SRX013098.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:10:35: #4 Write peak in narrowPeak format file... SRX013098.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:10:35: #4 Write summits bed file... SRX013098.05_summits.bed INFO @ Tue, 21 Apr 2015 12:10:35: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2014 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:10:36: #4 Write output xls file... SRX013098.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:10:36: #4 Write peak in narrowPeak format file... SRX013098.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:10:36: #4 Write summits bed file... SRX013098.20_summits.bed INFO @ Tue, 21 Apr 2015 12:10:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (339 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。