Job ID = 2161280 sra ファイルのダウンロード中... Completed: 546573K bytes transferred in 8 seconds (541396K bits/sec), in 2 files, 3 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 16381 0 16381 0 0 22527 0 --:--:-- --:--:-- --:--:-- 30561 100 34371 0 34371 0 0 47207 0 --:--:-- --:--:-- --:--:-- 64005 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 9492580 spots for /home/okishinya/chipatlas/results/dm3/SRX016146/SRR034700.sra Written 9492580 spots total Written 13490540 spots for /home/okishinya/chipatlas/results/dm3/SRX016146/SRR034701.sra Written 13490540 spots total fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:26 22983120 reads; of these: 22983120 (100.00%) were unpaired; of these: 616459 (2.68%) aligned 0 times 18456767 (80.31%) aligned exactly 1 time 3909894 (17.01%) aligned >1 times 97.32% overall alignment rate Time searching: 00:06:27 Overall time: 00:06:27 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] 11228977 / 22366661 = 0.5020 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 12:23:10: # Command line: callpeak -t SRX016146.bam -f BAM -g dm -n SRX016146.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX016146.20 # format = BAM # ChIP-seq file = ['SRX016146.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 12:23:10: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:23:10: # Command line: callpeak -t SRX016146.bam -f BAM -g dm -n SRX016146.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX016146.10 # format = BAM # ChIP-seq file = ['SRX016146.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 12:23:10: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:23:10: # Command line: callpeak -t SRX016146.bam -f BAM -g dm -n SRX016146.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX016146.05 # format = BAM # ChIP-seq file = ['SRX016146.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 12:23:10: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:23:10: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:23:10: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:23:10: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:23:15: 1000000 INFO @ Tue, 21 Apr 2015 12:23:15: 1000000 INFO @ Tue, 21 Apr 2015 12:23:15: 1000000 INFO @ Tue, 21 Apr 2015 12:23:21: 2000000 INFO @ Tue, 21 Apr 2015 12:23:21: 2000000 INFO @ Tue, 21 Apr 2015 12:23:21: 2000000 INFO @ Tue, 21 Apr 2015 12:23:27: 3000000 INFO @ Tue, 21 Apr 2015 12:23:27: 3000000 INFO @ Tue, 21 Apr 2015 12:23:27: 3000000 INFO @ Tue, 21 Apr 2015 12:23:32: 4000000 INFO @ Tue, 21 Apr 2015 12:23:32: 4000000 INFO @ Tue, 21 Apr 2015 12:23:32: 4000000 INFO @ Tue, 21 Apr 2015 12:23:38: 5000000 INFO @ Tue, 21 Apr 2015 12:23:38: 5000000 INFO @ Tue, 21 Apr 2015 12:23:38: 5000000 INFO @ Tue, 21 Apr 2015 12:23:44: 6000000 INFO @ Tue, 21 Apr 2015 12:23:44: 6000000 INFO @ Tue, 21 Apr 2015 12:23:44: 6000000 INFO @ Tue, 21 Apr 2015 12:23:49: 7000000 INFO @ Tue, 21 Apr 2015 12:23:49: 7000000 INFO @ Tue, 21 Apr 2015 12:23:49: 7000000 INFO @ Tue, 21 Apr 2015 12:23:55: 8000000 INFO @ Tue, 21 Apr 2015 12:23:55: 8000000 INFO @ Tue, 21 Apr 2015 12:23:55: 8000000 INFO @ Tue, 21 Apr 2015 12:24:01: 9000000 INFO @ Tue, 21 Apr 2015 12:24:01: 9000000 INFO @ Tue, 21 Apr 2015 12:24:01: 9000000 INFO @ Tue, 21 Apr 2015 12:24:06: 10000000 INFO @ Tue, 21 Apr 2015 12:24:06: 10000000 INFO @ Tue, 21 Apr 2015 12:24:06: 10000000 INFO @ Tue, 21 Apr 2015 12:24:12: 11000000 INFO @ Tue, 21 Apr 2015 12:24:12: 11000000 INFO @ Tue, 21 Apr 2015 12:24:12: 11000000 INFO @ Tue, 21 Apr 2015 12:24:13: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:24:13: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:24:13: #1 total tags in treatment: 11137684 INFO @ Tue, 21 Apr 2015 12:24:13: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:24:13: #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 12:24:13: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:24:13: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:24:13: #1 total tags in treatment: 11137684 INFO @ Tue, 21 Apr 2015 12:24:13: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:24:13: #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 12:24:13: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:24:13: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:24:13: #1 total tags in treatment: 11137684 INFO @ Tue, 21 Apr 2015 12:24:13: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:24:13: #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 12:24:15: #1 tags after filtering in treatment: 11136612 INFO @ Tue, 21 Apr 2015 12:24:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:24:15: #1 finished! INFO @ Tue, 21 Apr 2015 12:24:15: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:24:15: #1 tags after filtering in treatment: 11136612 INFO @ Tue, 21 Apr 2015 12:24:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:24:15: #1 finished! INFO @ Tue, 21 Apr 2015 12:24:15: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:24:15: #1 tags after filtering in treatment: 11136612 INFO @ Tue, 21 Apr 2015 12:24:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:24:15: #1 finished! INFO @ Tue, 21 Apr 2015 12:24:15: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:24:17: #2 number of paired peaks: 274 WARNING @ Tue, 21 Apr 2015 12:24:17: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Tue, 21 Apr 2015 12:24:17: start model_add_line... INFO @ Tue, 21 Apr 2015 12:24:17: #2 number of paired peaks: 274 WARNING @ Tue, 21 Apr 2015 12:24:17: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Tue, 21 Apr 2015 12:24:17: start model_add_line... INFO @ Tue, 21 Apr 2015 12:24:17: #2 number of paired peaks: 274 WARNING @ Tue, 21 Apr 2015 12:24:17: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Tue, 21 Apr 2015 12:24:17: start model_add_line... INFO @ Tue, 21 Apr 2015 12:24:19: start X-correlation... INFO @ Tue, 21 Apr 2015 12:24:19: end of X-cor INFO @ Tue, 21 Apr 2015 12:24:19: #2 finished! INFO @ Tue, 21 Apr 2015 12:24:19: #2 predicted fragment length is 85 bps INFO @ Tue, 21 Apr 2015 12:24:19: #2 alternative fragment length(s) may be 85 bps INFO @ Tue, 21 Apr 2015 12:24:19: #2.2 Generate R script for model : SRX016146.20_model.r INFO @ Tue, 21 Apr 2015 12:24:19: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:24:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:24:19: start X-correlation... INFO @ Tue, 21 Apr 2015 12:24:19: end of X-cor INFO @ Tue, 21 Apr 2015 12:24:19: #2 finished! INFO @ Tue, 21 Apr 2015 12:24:19: #2 predicted fragment length is 85 bps INFO @ Tue, 21 Apr 2015 12:24:19: #2 alternative fragment length(s) may be 85 bps INFO @ Tue, 21 Apr 2015 12:24:19: #2.2 Generate R script for model : SRX016146.10_model.r INFO @ Tue, 21 Apr 2015 12:24:19: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:24:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:24:20: start X-correlation... INFO @ Tue, 21 Apr 2015 12:24:20: end of X-cor INFO @ Tue, 21 Apr 2015 12:24:20: #2 finished! INFO @ Tue, 21 Apr 2015 12:24:20: #2 predicted fragment length is 85 bps INFO @ Tue, 21 Apr 2015 12:24:20: #2 alternative fragment length(s) may be 85 bps INFO @ Tue, 21 Apr 2015 12:24:20: #2.2 Generate R script for model : SRX016146.05_model.r INFO @ Tue, 21 Apr 2015 12:24:20: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:24:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:25:18: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:25:18: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:25:20: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:26:01: #4 Write output xls file... SRX016146.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:26:01: #4 Write peak in narrowPeak format file... SRX016146.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:26:01: #4 Write summits bed file... SRX016146.05_summits.bed INFO @ Tue, 21 Apr 2015 12:26:01: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2324 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:26:02: #4 Write output xls file... SRX016146.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:26:02: #4 Write peak in narrowPeak format file... SRX016146.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:26:02: #4 Write summits bed file... SRX016146.20_summits.bed INFO @ Tue, 21 Apr 2015 12:26:02: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (571 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:26:04: #4 Write output xls file... SRX016146.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:26:04: #4 Write peak in narrowPeak format file... SRX016146.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:26:04: #4 Write summits bed file... SRX016146.10_summits.bed INFO @ Tue, 21 Apr 2015 12:26:04: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (885 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。