Job ID = 2161187 sra ファイルのダウンロード中... Completed: 127827K bytes transferred in 4 seconds (233794K 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 15566 0 15566 0 0 22481 0 --:--:-- --:--:-- --:--:-- 31007 100 34866 0 34866 0 0 50287 0 --:--:-- --:--:-- --:--:-- 69316 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 4731386 spots for /home/okishinya/chipatlas/results/dm3/SRX013035/SRR030301.sra Written 4731386 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: 00:00:56 4731386 reads; of these: 4731386 (100.00%) were unpaired; of these: 649053 (13.72%) aligned 0 times 3689609 (77.98%) aligned exactly 1 time 392724 (8.30%) aligned >1 times 86.28% overall alignment rate Time searching: 00:00:57 Overall time: 00:00:57 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] 131502 / 4082333 = 0.0322 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 12:01:03: # Command line: callpeak -t SRX013035.bam -f BAM -g dm -n SRX013035.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013035.05 # format = BAM # ChIP-seq file = ['SRX013035.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 12:01:03: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:01:03: # Command line: callpeak -t SRX013035.bam -f BAM -g dm -n SRX013035.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013035.10 # format = BAM # ChIP-seq file = ['SRX013035.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 12:01:03: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:01:03: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:01:03: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:01:03: # Command line: callpeak -t SRX013035.bam -f BAM -g dm -n SRX013035.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013035.20 # format = BAM # ChIP-seq file = ['SRX013035.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 12:01:03: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:01:03: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:01:08: 1000000 INFO @ Tue, 21 Apr 2015 12:01:08: 1000000 INFO @ Tue, 21 Apr 2015 12:01:08: 1000000 INFO @ Tue, 21 Apr 2015 12:01:14: 2000000 INFO @ Tue, 21 Apr 2015 12:01:14: 2000000 INFO @ Tue, 21 Apr 2015 12:01:14: 2000000 INFO @ Tue, 21 Apr 2015 12:01:19: 3000000 INFO @ Tue, 21 Apr 2015 12:01:20: 3000000 INFO @ Tue, 21 Apr 2015 12:01:20: 3000000 INFO @ Tue, 21 Apr 2015 12:01:25: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:01:25: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:01:25: #1 total tags in treatment: 3950831 INFO @ Tue, 21 Apr 2015 12:01:25: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:01:25: #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 12:01:25: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:01:25: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:01:25: #1 total tags in treatment: 3950831 INFO @ Tue, 21 Apr 2015 12:01:25: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:01:25: #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 12:01:25: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:01:25: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:01:25: #1 total tags in treatment: 3950831 INFO @ Tue, 21 Apr 2015 12:01:25: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:01:25: #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 12:01:25: #1 tags after filtering in treatment: 3950694 INFO @ Tue, 21 Apr 2015 12:01:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:01:25: #1 finished! INFO @ Tue, 21 Apr 2015 12:01:25: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:01:26: #1 tags after filtering in treatment: 3950694 INFO @ Tue, 21 Apr 2015 12:01:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:01:26: #1 finished! INFO @ Tue, 21 Apr 2015 12:01:26: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:01:26: #1 tags after filtering in treatment: 3950694 INFO @ Tue, 21 Apr 2015 12:01:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:01:26: #1 finished! INFO @ Tue, 21 Apr 2015 12:01:26: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:01:26: #2 number of paired peaks: 640 WARNING @ Tue, 21 Apr 2015 12:01:26: Fewer paired peaks (640) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 640 pairs to build model! INFO @ Tue, 21 Apr 2015 12:01:26: start model_add_line... INFO @ Tue, 21 Apr 2015 12:01:27: #2 number of paired peaks: 640 WARNING @ Tue, 21 Apr 2015 12:01:27: Fewer paired peaks (640) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 640 pairs to build model! INFO @ Tue, 21 Apr 2015 12:01:27: start model_add_line... INFO @ Tue, 21 Apr 2015 12:01:27: #2 number of paired peaks: 640 WARNING @ Tue, 21 Apr 2015 12:01:27: Fewer paired peaks (640) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 640 pairs to build model! INFO @ Tue, 21 Apr 2015 12:01:27: start model_add_line... INFO @ Tue, 21 Apr 2015 12:01:28: start X-correlation... INFO @ Tue, 21 Apr 2015 12:01:28: end of X-cor INFO @ Tue, 21 Apr 2015 12:01:28: #2 finished! INFO @ Tue, 21 Apr 2015 12:01:28: #2 predicted fragment length is 160 bps INFO @ Tue, 21 Apr 2015 12:01:28: #2 alternative fragment length(s) may be 160 bps INFO @ Tue, 21 Apr 2015 12:01:28: #2.2 Generate R script for model : SRX013035.20_model.r INFO @ Tue, 21 Apr 2015 12:01:28: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:01:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:01:28: start X-correlation... INFO @ Tue, 21 Apr 2015 12:01:28: end of X-cor INFO @ Tue, 21 Apr 2015 12:01:28: #2 finished! INFO @ Tue, 21 Apr 2015 12:01:28: #2 predicted fragment length is 160 bps INFO @ Tue, 21 Apr 2015 12:01:28: #2 alternative fragment length(s) may be 160 bps INFO @ Tue, 21 Apr 2015 12:01:28: #2.2 Generate R script for model : SRX013035.05_model.r INFO @ Tue, 21 Apr 2015 12:01:28: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:01:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:01:28: start X-correlation... INFO @ Tue, 21 Apr 2015 12:01:28: end of X-cor INFO @ Tue, 21 Apr 2015 12:01:28: #2 finished! INFO @ Tue, 21 Apr 2015 12:01:28: #2 predicted fragment length is 160 bps INFO @ Tue, 21 Apr 2015 12:01:28: #2 alternative fragment length(s) may be 160 bps INFO @ Tue, 21 Apr 2015 12:01:28: #2.2 Generate R script for model : SRX013035.10_model.r INFO @ Tue, 21 Apr 2015 12:01:28: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:01:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:01:50: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:01:51: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:01:51: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:02:06: #4 Write output xls file... SRX013035.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:02:06: #4 Write peak in narrowPeak format file... SRX013035.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:02:06: #4 Write summits bed file... SRX013035.20_summits.bed INFO @ Tue, 21 Apr 2015 12:02:06: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (72 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:02:08: #4 Write output xls file... SRX013035.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:02:08: #4 Write peak in narrowPeak format file... SRX013035.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:02:08: #4 Write summits bed file... SRX013035.10_summits.bed INFO @ Tue, 21 Apr 2015 12:02:08: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (580 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:02:09: #4 Write output xls file... SRX013035.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:02:09: #4 Write peak in narrowPeak format file... SRX013035.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:02:09: #4 Write summits bed file... SRX013035.05_summits.bed INFO @ Tue, 21 Apr 2015 12:02:09: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (2289 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。