Job ID = 2165925 sra ファイルのダウンロード中... Completed: 342865K bytes transferred in 5 seconds (490188K 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 4007 0 4007 0 0 6366 0 --:--:-- --:--:-- --:--:-- 9127 100 36651 0 36651 0 0 44742 0 --:--:-- --:--:-- --:--:-- 58268 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 13720068 spots for /home/okishinya/chipatlas/results/sacCer3/SRX065607/SRR217310.sra Written 13720068 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: 00:01:21 13720068 reads; of these: 13720068 (100.00%) were unpaired; of these: 3674998 (26.79%) aligned 0 times 3601882 (26.25%) aligned exactly 1 time 6443188 (46.96%) aligned >1 times 73.21% overall alignment rate Time searching: 00:01:21 Overall time: 00:01:21 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] 8512542 / 10045070 = 0.8474 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 09:28:55: # Command line: callpeak -t SRX065607.bam -f BAM -g 12100000 -n SRX065607.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX065607.05 # format = BAM # ChIP-seq file = ['SRX065607.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 09:28:55: #1 read tag files... INFO @ Wed, 22 Apr 2015 09:28:55: #1 read treatment tags... INFO @ Wed, 22 Apr 2015 09:28:55: # Command line: callpeak -t SRX065607.bam -f BAM -g 12100000 -n SRX065607.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX065607.10 # format = BAM # ChIP-seq file = ['SRX065607.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 09:28:55: #1 read tag files... INFO @ Wed, 22 Apr 2015 09:28:55: # Command line: callpeak -t SRX065607.bam -f BAM -g 12100000 -n SRX065607.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX065607.20 # format = BAM # ChIP-seq file = ['SRX065607.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 09:28:55: #1 read treatment tags... INFO @ Wed, 22 Apr 2015 09:28:55: #1 read tag files... INFO @ Wed, 22 Apr 2015 09:28:55: #1 read treatment tags... INFO @ Wed, 22 Apr 2015 09:29:01: 1000000 INFO @ Wed, 22 Apr 2015 09:29:01: 1000000 INFO @ Wed, 22 Apr 2015 09:29:01: 1000000 INFO @ Wed, 22 Apr 2015 09:29:04: #1 tag size is determined as 36 bps INFO @ Wed, 22 Apr 2015 09:29:04: #1 tag size = 36 INFO @ Wed, 22 Apr 2015 09:29:04: #1 total tags in treatment: 1532528 INFO @ Wed, 22 Apr 2015 09:29:04: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2015 09:29:04: #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 09:29:04: #1 tags after filtering in treatment: 1532085 INFO @ Wed, 22 Apr 2015 09:29:04: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2015 09:29:04: #1 finished! INFO @ Wed, 22 Apr 2015 09:29:04: #2 Build Peak Model... INFO @ Wed, 22 Apr 2015 09:29:04: #1 tag size is determined as 36 bps INFO @ Wed, 22 Apr 2015 09:29:04: #1 tag size is determined as 36 bps INFO @ Wed, 22 Apr 2015 09:29:04: #1 tag size = 36 INFO @ Wed, 22 Apr 2015 09:29:04: #1 tag size = 36 INFO @ Wed, 22 Apr 2015 09:29:04: #1 total tags in treatment: 1532528 INFO @ Wed, 22 Apr 2015 09:29:04: #1 total tags in treatment: 1532528 INFO @ Wed, 22 Apr 2015 09:29:04: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2015 09:29:04: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2015 09:29:04: #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 09:29:04: #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 09:29:04: #2 number of paired peaks: 198 WARNING @ Wed, 22 Apr 2015 09:29:04: Fewer paired peaks (198) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 198 pairs to build model! INFO @ Wed, 22 Apr 2015 09:29:04: start model_add_line... INFO @ Wed, 22 Apr 2015 09:29:04: #1 tags after filtering in treatment: 1532085 INFO @ Wed, 22 Apr 2015 09:29:04: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2015 09:29:04: #1 finished! INFO @ Wed, 22 Apr 2015 09:29:04: #2 Build Peak Model... INFO @ Wed, 22 Apr 2015 09:29:04: #1 tags after filtering in treatment: 1532085 INFO @ Wed, 22 Apr 2015 09:29:04: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2015 09:29:04: #1 finished! INFO @ Wed, 22 Apr 2015 09:29:04: #2 Build Peak Model... INFO @ Wed, 22 Apr 2015 09:29:05: #2 number of paired peaks: 198 WARNING @ Wed, 22 Apr 2015 09:29:05: Fewer paired peaks (198) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 198 pairs to build model! INFO @ Wed, 22 Apr 2015 09:29:05: start model_add_line... INFO @ Wed, 22 Apr 2015 09:29:05: #2 number of paired peaks: 198 WARNING @ Wed, 22 Apr 2015 09:29:05: Fewer paired peaks (198) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 198 pairs to build model! INFO @ Wed, 22 Apr 2015 09:29:05: start model_add_line... INFO @ Wed, 22 Apr 2015 09:29:06: start X-correlation... INFO @ Wed, 22 Apr 2015 09:29:06: end of X-cor INFO @ Wed, 22 Apr 2015 09:29:06: #2 finished! INFO @ Wed, 22 Apr 2015 09:29:06: #2 predicted fragment length is 149 bps INFO @ Wed, 22 Apr 2015 09:29:06: #2 alternative fragment length(s) may be 149 bps INFO @ Wed, 22 Apr 2015 09:29:06: #2.2 Generate R script for model : SRX065607.05_model.r INFO @ Wed, 22 Apr 2015 09:29:06: #3 Call peaks... INFO @ Wed, 22 Apr 2015 09:29:06: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2015 09:29:07: start X-correlation... INFO @ Wed, 22 Apr 2015 09:29:07: end of X-cor INFO @ Wed, 22 Apr 2015 09:29:07: #2 finished! INFO @ Wed, 22 Apr 2015 09:29:07: #2 predicted fragment length is 149 bps INFO @ Wed, 22 Apr 2015 09:29:07: #2 alternative fragment length(s) may be 149 bps INFO @ Wed, 22 Apr 2015 09:29:07: #2.2 Generate R script for model : SRX065607.20_model.r INFO @ Wed, 22 Apr 2015 09:29:07: #3 Call peaks... INFO @ Wed, 22 Apr 2015 09:29:07: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2015 09:29:07: start X-correlation... INFO @ Wed, 22 Apr 2015 09:29:07: end of X-cor INFO @ Wed, 22 Apr 2015 09:29:07: #2 finished! INFO @ Wed, 22 Apr 2015 09:29:07: #2 predicted fragment length is 149 bps INFO @ Wed, 22 Apr 2015 09:29:07: #2 alternative fragment length(s) may be 149 bps INFO @ Wed, 22 Apr 2015 09:29:07: #2.2 Generate R script for model : SRX065607.10_model.r INFO @ Wed, 22 Apr 2015 09:29:07: #3 Call peaks... INFO @ Wed, 22 Apr 2015 09:29:07: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2015 09:29:15: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2015 09:29:16: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2015 09:29:16: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2015 09:29:22: #4 Write output xls file... SRX065607.20_peaks.xls INFO @ Wed, 22 Apr 2015 09:29:22: #4 Write peak in narrowPeak format file... SRX065607.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2015 09:29:22: #4 Write summits bed file... SRX065607.20_summits.bed INFO @ Wed, 22 Apr 2015 09:29:22: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (447 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2015 09:29:22: #4 Write output xls file... SRX065607.05_peaks.xls INFO @ Wed, 22 Apr 2015 09:29:22: #4 Write peak in narrowPeak format file... SRX065607.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2015 09:29:22: #4 Write summits bed file... SRX065607.05_summits.bed INFO @ Wed, 22 Apr 2015 09:29:22: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1073 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2015 09:29:22: #4 Write output xls file... SRX065607.10_peaks.xls INFO @ Wed, 22 Apr 2015 09:29:22: #4 Write peak in narrowPeak format file... SRX065607.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2015 09:29:22: #4 Write summits bed file... SRX065607.10_summits.bed INFO @ Wed, 22 Apr 2015 09:29:22: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (720 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。