Job ID = 2165879 sra ファイルのダウンロード中... Completed: 94018K bytes transferred in 4 seconds (176388K 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 14904 0 14904 0 0 20297 0 --:--:-- --:--:-- --:--:-- 27397 100 36613 0 36613 0 0 49796 0 --:--:-- --:--:-- --:--:-- 67179 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 4260207 spots for /home/okishinya/chipatlas/results/sacCer3/SRX021359/SRR051930.sra Written 4260207 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: 00:00:25 4260207 reads; of these: 4260207 (100.00%) were unpaired; of these: 2347278 (55.10%) aligned 0 times 1289309 (30.26%) aligned exactly 1 time 623620 (14.64%) aligned >1 times 44.90% overall alignment rate Time searching: 00:00:25 Overall time: 00:00:25 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdupse_core] 1255287 / 1912929 = 0.6562 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 @ Wed, 22 Apr 2015 09:18:39: # Command line: callpeak -t SRX021359.bam -f BAM -g 12100000 -n SRX021359.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX021359.20 # format = BAM # ChIP-seq file = ['SRX021359.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Wed, 22 Apr 2015 09:18:39: #1 read tag files... INFO @ Wed, 22 Apr 2015 09:18:39: # Command line: callpeak -t SRX021359.bam -f BAM -g 12100000 -n SRX021359.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX021359.05 # format = BAM # ChIP-seq file = ['SRX021359.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Wed, 22 Apr 2015 09:18:39: #1 read treatment tags... INFO @ Wed, 22 Apr 2015 09:18:39: #1 read tag files... INFO @ Wed, 22 Apr 2015 09:18:39: #1 read treatment tags... INFO @ Wed, 22 Apr 2015 09:18:39: # Command line: callpeak -t SRX021359.bam -f BAM -g 12100000 -n SRX021359.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX021359.10 # format = BAM # ChIP-seq file = ['SRX021359.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Wed, 22 Apr 2015 09:18:39: #1 read tag files... INFO @ Wed, 22 Apr 2015 09:18:39: #1 read treatment tags... INFO @ Wed, 22 Apr 2015 09:18:42: #1 tag size is determined as 35 bps INFO @ Wed, 22 Apr 2015 09:18:42: #1 tag size = 35 INFO @ Wed, 22 Apr 2015 09:18:42: #1 total tags in treatment: 657642 INFO @ Wed, 22 Apr 2015 09:18:42: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2015 09:18:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2015 09:18:42: #1 tag size is determined as 35 bps INFO @ Wed, 22 Apr 2015 09:18:42: #1 tag size = 35 INFO @ Wed, 22 Apr 2015 09:18:42: #1 total tags in treatment: 657642 INFO @ Wed, 22 Apr 2015 09:18:42: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2015 09:18:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2015 09:18:42: #1 tags after filtering in treatment: 657127 INFO @ Wed, 22 Apr 2015 09:18:42: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2015 09:18:42: #1 finished! INFO @ Wed, 22 Apr 2015 09:18:42: #2 Build Peak Model... INFO @ Wed, 22 Apr 2015 09:18:42: #1 tags after filtering in treatment: 657127 INFO @ Wed, 22 Apr 2015 09:18:42: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2015 09:18:42: #1 finished! INFO @ Wed, 22 Apr 2015 09:18:42: #2 Build Peak Model... INFO @ Wed, 22 Apr 2015 09:18:42: #1 tag size is determined as 35 bps INFO @ Wed, 22 Apr 2015 09:18:42: #1 tag size = 35 INFO @ Wed, 22 Apr 2015 09:18:42: #1 total tags in treatment: 657642 INFO @ Wed, 22 Apr 2015 09:18:42: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2015 09:18:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2015 09:18:42: #2 number of paired peaks: 296 WARNING @ Wed, 22 Apr 2015 09:18:42: Fewer paired peaks (296) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 296 pairs to build model! INFO @ Wed, 22 Apr 2015 09:18:42: start model_add_line... INFO @ Wed, 22 Apr 2015 09:18:42: #1 tags after filtering in treatment: 657127 INFO @ Wed, 22 Apr 2015 09:18:42: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2015 09:18:42: #1 finished! INFO @ Wed, 22 Apr 2015 09:18:42: #2 Build Peak Model... INFO @ Wed, 22 Apr 2015 09:18:42: #2 number of paired peaks: 296 WARNING @ Wed, 22 Apr 2015 09:18:42: Fewer paired peaks (296) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 296 pairs to build model! INFO @ Wed, 22 Apr 2015 09:18:42: start model_add_line... INFO @ Wed, 22 Apr 2015 09:18:42: #2 number of paired peaks: 296 WARNING @ Wed, 22 Apr 2015 09:18:42: Fewer paired peaks (296) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 296 pairs to build model! INFO @ Wed, 22 Apr 2015 09:18:42: start model_add_line... INFO @ Wed, 22 Apr 2015 09:18:45: start X-correlation... INFO @ Wed, 22 Apr 2015 09:18:45: end of X-cor INFO @ Wed, 22 Apr 2015 09:18:45: #2 finished! INFO @ Wed, 22 Apr 2015 09:18:45: #2 predicted fragment length is 211 bps INFO @ Wed, 22 Apr 2015 09:18:45: #2 alternative fragment length(s) may be 211 bps INFO @ Wed, 22 Apr 2015 09:18:45: #2.2 Generate R script for model : SRX021359.10_model.r INFO @ Wed, 22 Apr 2015 09:18:45: #3 Call peaks... INFO @ Wed, 22 Apr 2015 09:18:45: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2015 09:18:45: start X-correlation... INFO @ Wed, 22 Apr 2015 09:18:45: end of X-cor INFO @ Wed, 22 Apr 2015 09:18:45: #2 finished! INFO @ Wed, 22 Apr 2015 09:18:45: #2 predicted fragment length is 211 bps INFO @ Wed, 22 Apr 2015 09:18:45: #2 alternative fragment length(s) may be 211 bps INFO @ Wed, 22 Apr 2015 09:18:45: #2.2 Generate R script for model : SRX021359.20_model.r INFO @ Wed, 22 Apr 2015 09:18:45: #3 Call peaks... INFO @ Wed, 22 Apr 2015 09:18:45: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2015 09:18:45: start X-correlation... INFO @ Wed, 22 Apr 2015 09:18:45: end of X-cor INFO @ Wed, 22 Apr 2015 09:18:45: #2 finished! INFO @ Wed, 22 Apr 2015 09:18:45: #2 predicted fragment length is 211 bps INFO @ Wed, 22 Apr 2015 09:18:45: #2 alternative fragment length(s) may be 211 bps INFO @ Wed, 22 Apr 2015 09:18:45: #2.2 Generate R script for model : SRX021359.05_model.r INFO @ Wed, 22 Apr 2015 09:18:45: #3 Call peaks... INFO @ Wed, 22 Apr 2015 09:18:45: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2015 09:18:50: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2015 09:18:50: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2015 09:18:50: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2015 09:18:53: #4 Write output xls file... SRX021359.20_peaks.xls INFO @ Wed, 22 Apr 2015 09:18:53: #4 Write peak in narrowPeak format file... SRX021359.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2015 09:18:53: #4 Write summits bed file... SRX021359.20_summits.bed INFO @ Wed, 22 Apr 2015 09:18:53: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (258 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Wed, 22 Apr 2015 09:18:53: #4 Write output xls file... SRX021359.10_peaks.xls INFO @ Wed, 22 Apr 2015 09:18:53: #4 Write peak in narrowPeak format file... SRX021359.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2015 09:18:53: #4 Write summits bed file... SRX021359.10_summits.bed INFO @ Wed, 22 Apr 2015 09:18:53: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (360 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2015 09:18:54: #4 Write output xls file... SRX021359.05_peaks.xls INFO @ Wed, 22 Apr 2015 09:18:54: #4 Write peak in narrowPeak format file... SRX021359.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2015 09:18:54: #4 Write summits bed file... SRX021359.05_summits.bed INFO @ Wed, 22 Apr 2015 09:18:54: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (576 records, 4 fields): 3 millis CompletedMACS2peakCalling