Job ID = 2161273 sra ファイルのダウンロード中... Completed: 426197K bytes transferred in 7 seconds (447603K 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 --:--:-- --:--:-- --:--:-- 0 101 5467 0 5467 0 0 10285 0 --:--:-- --:--:-- --:--:-- 16032 100 35513 0 35513 0 0 49257 0 --:--:-- --:--:-- --:--:-- 66879 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 6451854 spots for /home/okishinya/chipatlas/results/dm3/SRX015109/SRR032455.sra Written 6451854 spots total Written 9659716 spots for /home/okishinya/chipatlas/results/dm3/SRX015109/SRR032456.sra Written 9659716 spots total 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: 00:04:00 16111570 reads; of these: 16111570 (100.00%) were unpaired; of these: 3998954 (24.82%) aligned 0 times 8955727 (55.59%) aligned exactly 1 time 3156889 (19.59%) aligned >1 times 75.18% overall alignment rate Time searching: 00:04:00 Overall time: 00:04:00 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] 1187381 / 12112616 = 0.0980 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 12:18:00: # Command line: callpeak -t SRX015109.bam -f BAM -g dm -n SRX015109.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX015109.10 # format = BAM # ChIP-seq file = ['SRX015109.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 12:18:00: # Command line: callpeak -t SRX015109.bam -f BAM -g dm -n SRX015109.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX015109.05 # format = BAM # ChIP-seq file = ['SRX015109.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 12:18:00: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:18:00: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:18:00: # Command line: callpeak -t SRX015109.bam -f BAM -g dm -n SRX015109.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX015109.20 # format = BAM # ChIP-seq file = ['SRX015109.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 12:18:00: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:18:00: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:18:00: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:18:00: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:18:06: 1000000 INFO @ Tue, 21 Apr 2015 12:18:06: 1000000 INFO @ Tue, 21 Apr 2015 12:18:06: 1000000 INFO @ Tue, 21 Apr 2015 12:18:11: 2000000 INFO @ Tue, 21 Apr 2015 12:18:12: 2000000 INFO @ Tue, 21 Apr 2015 12:18:12: 2000000 INFO @ Tue, 21 Apr 2015 12:18:17: 3000000 INFO @ Tue, 21 Apr 2015 12:18:18: 3000000 INFO @ Tue, 21 Apr 2015 12:18:18: 3000000 INFO @ Tue, 21 Apr 2015 12:18:23: 4000000 INFO @ Tue, 21 Apr 2015 12:18:23: 4000000 INFO @ Tue, 21 Apr 2015 12:18:24: 4000000 INFO @ Tue, 21 Apr 2015 12:18:29: 5000000 INFO @ Tue, 21 Apr 2015 12:18:29: 5000000 INFO @ Tue, 21 Apr 2015 12:18:30: 5000000 INFO @ Tue, 21 Apr 2015 12:18:35: 6000000 INFO @ Tue, 21 Apr 2015 12:18:35: 6000000 INFO @ Tue, 21 Apr 2015 12:18:36: 6000000 INFO @ Tue, 21 Apr 2015 12:18:41: 7000000 INFO @ Tue, 21 Apr 2015 12:18:41: 7000000 INFO @ Tue, 21 Apr 2015 12:18:42: 7000000 INFO @ Tue, 21 Apr 2015 12:18:47: 8000000 INFO @ Tue, 21 Apr 2015 12:18:47: 8000000 INFO @ Tue, 21 Apr 2015 12:18:48: 8000000 INFO @ Tue, 21 Apr 2015 12:18:53: 9000000 INFO @ Tue, 21 Apr 2015 12:18:53: 9000000 INFO @ Tue, 21 Apr 2015 12:18:54: 9000000 INFO @ Tue, 21 Apr 2015 12:18:59: 10000000 INFO @ Tue, 21 Apr 2015 12:18:59: 10000000 INFO @ Tue, 21 Apr 2015 12:19:00: 10000000 INFO @ Tue, 21 Apr 2015 12:19:04: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:19:04: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:19:04: #1 total tags in treatment: 10925235 INFO @ Tue, 21 Apr 2015 12:19:04: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:19:04: #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 12:19:05: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:19:05: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:19:05: #1 total tags in treatment: 10925235 INFO @ Tue, 21 Apr 2015 12:19:05: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:19:05: #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 12:19:06: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:19:06: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:19:06: #1 total tags in treatment: 10925235 INFO @ Tue, 21 Apr 2015 12:19:06: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:19:06: #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 12:19:06: #1 tags after filtering in treatment: 10923926 INFO @ Tue, 21 Apr 2015 12:19:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:19:06: #1 finished! INFO @ Tue, 21 Apr 2015 12:19:06: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:19:07: #1 tags after filtering in treatment: 10923926 INFO @ Tue, 21 Apr 2015 12:19:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:19:07: #1 finished! INFO @ Tue, 21 Apr 2015 12:19:07: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:19:08: #1 tags after filtering in treatment: 10923926 INFO @ Tue, 21 Apr 2015 12:19:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:19:08: #1 finished! INFO @ Tue, 21 Apr 2015 12:19:08: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:19:09: #2 number of paired peaks: 656 WARNING @ Tue, 21 Apr 2015 12:19:09: Fewer paired peaks (656) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 656 pairs to build model! INFO @ Tue, 21 Apr 2015 12:19:09: start model_add_line... INFO @ Tue, 21 Apr 2015 12:19:09: #2 number of paired peaks: 656 WARNING @ Tue, 21 Apr 2015 12:19:09: Fewer paired peaks (656) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 656 pairs to build model! INFO @ Tue, 21 Apr 2015 12:19:09: start model_add_line... INFO @ Tue, 21 Apr 2015 12:19:10: #2 number of paired peaks: 656 WARNING @ Tue, 21 Apr 2015 12:19:10: Fewer paired peaks (656) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 656 pairs to build model! INFO @ Tue, 21 Apr 2015 12:19:10: start model_add_line... INFO @ Tue, 21 Apr 2015 12:19:14: start X-correlation... INFO @ Tue, 21 Apr 2015 12:19:14: end of X-cor INFO @ Tue, 21 Apr 2015 12:19:14: #2 finished! INFO @ Tue, 21 Apr 2015 12:19:14: #2 predicted fragment length is 100 bps INFO @ Tue, 21 Apr 2015 12:19:14: #2 alternative fragment length(s) may be 100 bps INFO @ Tue, 21 Apr 2015 12:19:14: #2.2 Generate R script for model : SRX015109.05_model.r INFO @ Tue, 21 Apr 2015 12:19:14: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:19:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:19:14: start X-correlation... INFO @ Tue, 21 Apr 2015 12:19:14: end of X-cor INFO @ Tue, 21 Apr 2015 12:19:14: #2 finished! INFO @ Tue, 21 Apr 2015 12:19:14: #2 predicted fragment length is 100 bps INFO @ Tue, 21 Apr 2015 12:19:14: #2 alternative fragment length(s) may be 100 bps INFO @ Tue, 21 Apr 2015 12:19:14: #2.2 Generate R script for model : SRX015109.10_model.r INFO @ Tue, 21 Apr 2015 12:19:14: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:19:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:19:15: start X-correlation... INFO @ Tue, 21 Apr 2015 12:19:15: end of X-cor INFO @ Tue, 21 Apr 2015 12:19:15: #2 finished! INFO @ Tue, 21 Apr 2015 12:19:15: #2 predicted fragment length is 100 bps INFO @ Tue, 21 Apr 2015 12:19:15: #2 alternative fragment length(s) may be 100 bps INFO @ Tue, 21 Apr 2015 12:19:15: #2.2 Generate R script for model : SRX015109.20_model.r INFO @ Tue, 21 Apr 2015 12:19:15: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:19:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:20:12: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:20:16: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:20:17: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:20:57: #4 Write output xls file... SRX015109.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:20:57: #4 Write peak in narrowPeak format file... SRX015109.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:20:57: #4 Write summits bed file... SRX015109.10_summits.bed INFO @ Tue, 21 Apr 2015 12:20:57: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3575 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:20:59: #4 Write output xls file... SRX015109.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:20:59: #4 Write peak in narrowPeak format file... SRX015109.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:20:59: #4 Write summits bed file... SRX015109.20_summits.bed INFO @ Tue, 21 Apr 2015 12:20:59: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (2070 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:21:06: #4 Write output xls file... SRX015109.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:21:06: #4 Write peak in narrowPeak format file... SRX015109.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:21:06: #4 Write summits bed file... SRX015109.05_summits.bed INFO @ Tue, 21 Apr 2015 12:21:07: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5795 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。