Job ID = 2165877 sra ファイルのダウンロード中... Completed: 156417K bytes transferred in 4 seconds (258430K 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 4007 0 4007 0 0 7903 0 --:--:-- --:--:-- --:--:-- 12640 100 35839 0 35839 0 0 51415 0 --:--:-- --:--:-- --:--:-- 70688 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 2697707 spots for /home/okishinya/chipatlas/results/sacCer3/SRX016026/SRR034476.sra Written 2697707 spots total Written 4001069 spots for /home/okishinya/chipatlas/results/sacCer3/SRX016026/SRR034475.sra Written 4001069 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: 00:00:54 6698776 reads; of these: 6698776 (100.00%) were unpaired; of these: 2072056 (30.93%) aligned 0 times 2769736 (41.35%) aligned exactly 1 time 1856984 (27.72%) aligned >1 times 69.07% overall alignment rate Time searching: 00:00:54 Overall time: 00:00:54 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] 2248584 / 4626720 = 0.4860 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 09:19:14: # Command line: callpeak -t SRX016026.bam -f BAM -g 12100000 -n SRX016026.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX016026.10 # format = BAM # ChIP-seq file = ['SRX016026.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 09:19:14: #1 read tag files... INFO @ Wed, 22 Apr 2015 09:19:14: #1 read treatment tags... INFO @ Wed, 22 Apr 2015 09:19:14: # Command line: callpeak -t SRX016026.bam -f BAM -g 12100000 -n SRX016026.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX016026.20 # format = BAM # ChIP-seq file = ['SRX016026.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 09:19:14: # Command line: callpeak -t SRX016026.bam -f BAM -g 12100000 -n SRX016026.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX016026.05 # format = BAM # ChIP-seq file = ['SRX016026.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 09:19:14: #1 read tag files... INFO @ Wed, 22 Apr 2015 09:19:14: #1 read tag files... INFO @ Wed, 22 Apr 2015 09:19:14: #1 read treatment tags... INFO @ Wed, 22 Apr 2015 09:19:14: #1 read treatment tags... INFO @ Wed, 22 Apr 2015 09:19:19: 1000000 INFO @ Wed, 22 Apr 2015 09:19:19: 1000000 INFO @ Wed, 22 Apr 2015 09:19:19: 1000000 INFO @ Wed, 22 Apr 2015 09:19:25: 2000000 INFO @ Wed, 22 Apr 2015 09:19:25: 2000000 INFO @ Wed, 22 Apr 2015 09:19:25: 2000000 INFO @ Wed, 22 Apr 2015 09:19:27: #1 tag size is determined as 39 bps INFO @ Wed, 22 Apr 2015 09:19:27: #1 tag size = 39 INFO @ Wed, 22 Apr 2015 09:19:27: #1 total tags in treatment: 2378136 INFO @ Wed, 22 Apr 2015 09:19:27: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2015 09:19:27: #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 09:19:27: #1 tag size is determined as 39 bps INFO @ Wed, 22 Apr 2015 09:19:27: #1 tag size = 39 INFO @ Wed, 22 Apr 2015 09:19:27: #1 total tags in treatment: 2378136 INFO @ Wed, 22 Apr 2015 09:19:27: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2015 09:19:27: #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 09:19:27: #1 tag size is determined as 39 bps INFO @ Wed, 22 Apr 2015 09:19:27: #1 tag size = 39 INFO @ Wed, 22 Apr 2015 09:19:27: #1 total tags in treatment: 2378136 INFO @ Wed, 22 Apr 2015 09:19:27: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2015 09:19:27: #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 09:19:27: #1 tags after filtering in treatment: 2376316 INFO @ Wed, 22 Apr 2015 09:19:27: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2015 09:19:27: #1 finished! INFO @ Wed, 22 Apr 2015 09:19:27: #2 Build Peak Model... INFO @ Wed, 22 Apr 2015 09:19:28: #1 tags after filtering in treatment: 2376316 INFO @ Wed, 22 Apr 2015 09:19:28: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2015 09:19:28: #1 finished! INFO @ Wed, 22 Apr 2015 09:19:28: #2 Build Peak Model... INFO @ Wed, 22 Apr 2015 09:19:28: #1 tags after filtering in treatment: 2376316 INFO @ Wed, 22 Apr 2015 09:19:28: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2015 09:19:28: #1 finished! INFO @ Wed, 22 Apr 2015 09:19:28: #2 Build Peak Model... INFO @ Wed, 22 Apr 2015 09:19:28: #2 number of paired peaks: 177 WARNING @ Wed, 22 Apr 2015 09:19:28: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Wed, 22 Apr 2015 09:19:28: start model_add_line... INFO @ Wed, 22 Apr 2015 09:19:28: #2 number of paired peaks: 177 WARNING @ Wed, 22 Apr 2015 09:19:28: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Wed, 22 Apr 2015 09:19:28: start model_add_line... INFO @ Wed, 22 Apr 2015 09:19:28: #2 number of paired peaks: 177 WARNING @ Wed, 22 Apr 2015 09:19:28: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Wed, 22 Apr 2015 09:19:28: start model_add_line... INFO @ Wed, 22 Apr 2015 09:19:31: start X-correlation... INFO @ Wed, 22 Apr 2015 09:19:31: end of X-cor INFO @ Wed, 22 Apr 2015 09:19:31: #2 finished! INFO @ Wed, 22 Apr 2015 09:19:31: #2 predicted fragment length is 104 bps INFO @ Wed, 22 Apr 2015 09:19:31: #2 alternative fragment length(s) may be 4,87,104 bps INFO @ Wed, 22 Apr 2015 09:19:31: #2.2 Generate R script for model : SRX016026.05_model.r INFO @ Wed, 22 Apr 2015 09:19:31: #3 Call peaks... INFO @ Wed, 22 Apr 2015 09:19:31: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2015 09:19:31: start X-correlation... INFO @ Wed, 22 Apr 2015 09:19:31: end of X-cor INFO @ Wed, 22 Apr 2015 09:19:31: #2 finished! INFO @ Wed, 22 Apr 2015 09:19:31: #2 predicted fragment length is 104 bps INFO @ Wed, 22 Apr 2015 09:19:31: #2 alternative fragment length(s) may be 4,87,104 bps INFO @ Wed, 22 Apr 2015 09:19:31: #2.2 Generate R script for model : SRX016026.10_model.r INFO @ Wed, 22 Apr 2015 09:19:31: #3 Call peaks... INFO @ Wed, 22 Apr 2015 09:19:31: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2015 09:19:31: start X-correlation... INFO @ Wed, 22 Apr 2015 09:19:31: end of X-cor INFO @ Wed, 22 Apr 2015 09:19:31: #2 finished! INFO @ Wed, 22 Apr 2015 09:19:31: #2 predicted fragment length is 104 bps INFO @ Wed, 22 Apr 2015 09:19:31: #2 alternative fragment length(s) may be 4,87,104 bps INFO @ Wed, 22 Apr 2015 09:19:31: #2.2 Generate R script for model : SRX016026.20_model.r INFO @ Wed, 22 Apr 2015 09:19:31: #3 Call peaks... INFO @ Wed, 22 Apr 2015 09:19:31: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2015 09:19:43: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2015 09:19:44: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2015 09:19:44: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2015 09:19:51: #4 Write output xls file... SRX016026.20_peaks.xls INFO @ Wed, 22 Apr 2015 09:19:51: #4 Write peak in narrowPeak format file... SRX016026.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2015 09:19:51: #4 Write summits bed file... SRX016026.20_summits.bed INFO @ Wed, 22 Apr 2015 09:19:51: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (299 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2015 09:19:52: #4 Write output xls file... SRX016026.05_peaks.xls INFO @ Wed, 22 Apr 2015 09:19:52: #4 Write peak in narrowPeak format file... SRX016026.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2015 09:19:52: #4 Write summits bed file... SRX016026.05_summits.bed INFO @ Wed, 22 Apr 2015 09:19:52: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (724 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2015 09:19:53: #4 Write output xls file... SRX016026.10_peaks.xls INFO @ Wed, 22 Apr 2015 09:19:53: #4 Write peak in narrowPeak format file... SRX016026.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2015 09:19:53: #4 Write summits bed file... SRX016026.10_summits.bed INFO @ Wed, 22 Apr 2015 09:19:53: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (444 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。