Job ID = 2162378 sra ファイルのダウンロード中... Completed: 473158K bytes transferred in 7 seconds (504736K 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 13456 0 13456 0 0 21513 0 --:--:-- --:--:-- --:--:-- 30933 100 36802 0 36802 0 0 45152 0 --:--:-- --:--:-- --:--:-- 58977 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 17747019 spots for /home/okishinya/chipatlas/results/dm3/SRX054534/SRR167349.sra Written 17747019 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: 00:04:41 17747019 reads; of these: 17747019 (100.00%) were unpaired; of these: 3907422 (22.02%) aligned 0 times 9945430 (56.04%) aligned exactly 1 time 3894167 (21.94%) aligned >1 times 77.98% overall alignment rate Time searching: 00:04:41 Overall time: 00:04:41 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] 4770465 / 13839597 = 0.3447 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 13:45:25: # Command line: callpeak -t SRX054534.bam -f BAM -g dm -n SRX054534.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX054534.10 # format = BAM # ChIP-seq file = ['SRX054534.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 13:45:25: # Command line: callpeak -t SRX054534.bam -f BAM -g dm -n SRX054534.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX054534.05 # format = BAM # ChIP-seq file = ['SRX054534.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 13:45:25: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:45:25: # Command line: callpeak -t SRX054534.bam -f BAM -g dm -n SRX054534.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX054534.20 # format = BAM # ChIP-seq file = ['SRX054534.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 13:45:25: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:45:25: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:45:25: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:45:25: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:45:25: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:45:30: 1000000 INFO @ Tue, 21 Apr 2015 13:45:30: 1000000 INFO @ Tue, 21 Apr 2015 13:45:30: 1000000 INFO @ Tue, 21 Apr 2015 13:45:34: 2000000 INFO @ Tue, 21 Apr 2015 13:45:35: 2000000 INFO @ Tue, 21 Apr 2015 13:45:35: 2000000 INFO @ Tue, 21 Apr 2015 13:45:39: 3000000 INFO @ Tue, 21 Apr 2015 13:45:39: 3000000 INFO @ Tue, 21 Apr 2015 13:45:40: 3000000 INFO @ Tue, 21 Apr 2015 13:45:44: 4000000 INFO @ Tue, 21 Apr 2015 13:45:44: 4000000 INFO @ Tue, 21 Apr 2015 13:45:45: 4000000 INFO @ Tue, 21 Apr 2015 13:45:49: 5000000 INFO @ Tue, 21 Apr 2015 13:45:50: 5000000 INFO @ Tue, 21 Apr 2015 13:45:50: 5000000 INFO @ Tue, 21 Apr 2015 13:45:54: 6000000 INFO @ Tue, 21 Apr 2015 13:45:55: 6000000 INFO @ Tue, 21 Apr 2015 13:45:55: 6000000 INFO @ Tue, 21 Apr 2015 13:45:59: 7000000 INFO @ Tue, 21 Apr 2015 13:46:00: 7000000 INFO @ Tue, 21 Apr 2015 13:46:01: 7000000 INFO @ Tue, 21 Apr 2015 13:46:04: 8000000 INFO @ Tue, 21 Apr 2015 13:46:05: 8000000 INFO @ Tue, 21 Apr 2015 13:46:06: 8000000 INFO @ Tue, 21 Apr 2015 13:46:09: 9000000 INFO @ Tue, 21 Apr 2015 13:46:09: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:46:09: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:46:09: #1 total tags in treatment: 9069132 INFO @ Tue, 21 Apr 2015 13:46:09: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:46:09: #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 13:46:10: 9000000 INFO @ Tue, 21 Apr 2015 13:46:10: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:46:10: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:46:10: #1 total tags in treatment: 9069132 INFO @ Tue, 21 Apr 2015 13:46:10: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:46:10: #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 13:46:11: #1 tags after filtering in treatment: 9066756 INFO @ Tue, 21 Apr 2015 13:46:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:46:11: #1 finished! INFO @ Tue, 21 Apr 2015 13:46:11: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:46:11: 9000000 INFO @ Tue, 21 Apr 2015 13:46:12: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:46:12: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:46:12: #1 total tags in treatment: 9069132 INFO @ Tue, 21 Apr 2015 13:46:12: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:46:12: #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 13:46:12: #1 tags after filtering in treatment: 9066756 INFO @ Tue, 21 Apr 2015 13:46:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:46:12: #1 finished! INFO @ Tue, 21 Apr 2015 13:46:12: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:46:12: #2 number of paired peaks: 168 WARNING @ Tue, 21 Apr 2015 13:46:12: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Tue, 21 Apr 2015 13:46:12: start model_add_line... INFO @ Tue, 21 Apr 2015 13:46:13: #1 tags after filtering in treatment: 9066756 INFO @ Tue, 21 Apr 2015 13:46:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:46:13: #1 finished! INFO @ Tue, 21 Apr 2015 13:46:13: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:46:14: #2 number of paired peaks: 168 WARNING @ Tue, 21 Apr 2015 13:46:14: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Tue, 21 Apr 2015 13:46:14: start model_add_line... INFO @ Tue, 21 Apr 2015 13:46:14: start X-correlation... INFO @ Tue, 21 Apr 2015 13:46:14: end of X-cor INFO @ Tue, 21 Apr 2015 13:46:14: #2 finished! INFO @ Tue, 21 Apr 2015 13:46:14: #2 predicted fragment length is 81 bps INFO @ Tue, 21 Apr 2015 13:46:14: #2 alternative fragment length(s) may be 81,133,162,195,225,253,439,540 bps INFO @ Tue, 21 Apr 2015 13:46:14: #2.2 Generate R script for model : SRX054534.20_model.r INFO @ Tue, 21 Apr 2015 13:46:14: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:46:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:46:15: #2 number of paired peaks: 168 WARNING @ Tue, 21 Apr 2015 13:46:15: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Tue, 21 Apr 2015 13:46:15: start model_add_line... INFO @ Tue, 21 Apr 2015 13:46:15: start X-correlation... INFO @ Tue, 21 Apr 2015 13:46:15: end of X-cor INFO @ Tue, 21 Apr 2015 13:46:15: #2 finished! INFO @ Tue, 21 Apr 2015 13:46:15: #2 predicted fragment length is 81 bps INFO @ Tue, 21 Apr 2015 13:46:15: #2 alternative fragment length(s) may be 81,133,162,195,225,253,439,540 bps INFO @ Tue, 21 Apr 2015 13:46:15: #2.2 Generate R script for model : SRX054534.10_model.r INFO @ Tue, 21 Apr 2015 13:46:15: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:46:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:46:17: start X-correlation... INFO @ Tue, 21 Apr 2015 13:46:17: end of X-cor INFO @ Tue, 21 Apr 2015 13:46:17: #2 finished! INFO @ Tue, 21 Apr 2015 13:46:17: #2 predicted fragment length is 81 bps INFO @ Tue, 21 Apr 2015 13:46:17: #2 alternative fragment length(s) may be 81,133,162,195,225,253,439,540 bps INFO @ Tue, 21 Apr 2015 13:46:17: #2.2 Generate R script for model : SRX054534.05_model.r INFO @ Tue, 21 Apr 2015 13:46:17: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:46:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:47:04: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:47:04: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:47:10: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:47:40: #4 Write output xls file... SRX054534.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:47:40: #4 Write peak in narrowPeak format file... SRX054534.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:47:40: #4 Write summits bed file... SRX054534.20_summits.bed INFO @ Tue, 21 Apr 2015 13:47:40: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (205 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:47:42: #4 Write output xls file... SRX054534.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:47:42: #4 Write peak in narrowPeak format file... SRX054534.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:47:42: #4 Write summits bed file... SRX054534.10_summits.bed INFO @ Tue, 21 Apr 2015 13:47:42: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1030 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:47:50: #4 Write output xls file... SRX054534.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:47:50: #4 Write peak in narrowPeak format file... SRX054534.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:47:50: #4 Write summits bed file... SRX054534.05_summits.bed INFO @ Tue, 21 Apr 2015 13:47:50: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3115 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。