Job ID = 2237075 sra ファイルのダウンロード中... Completed: 129077K bytes transferred in 6 seconds (170252K 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 36833 0 36833 0 0 43064 0 --:--:-- --:--:-- --:--:-- 55471 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 6857333 spots for /home/okishinya/chipatlas/results/ce10/SRX113617/SRR393717.sra Written 6857333 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: 00:02:00 6857333 reads; of these: 6857333 (100.00%) were unpaired; of these: 384035 (5.60%) aligned 0 times 4529836 (66.06%) aligned exactly 1 time 1943462 (28.34%) aligned >1 times 94.40% overall alignment rate Time searching: 00:02:00 Overall time: 00:02:01 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 2113322 / 6473298 = 0.3265 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 @ Thu, 30 Apr 2015 11:29:48: # Command line: callpeak -t SRX113617.bam -f BAM -g ce -n SRX113617.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX113617.05 # format = BAM # ChIP-seq file = ['SRX113617.bam'] # control file = None # effective genome size = 9.00e+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 @ Thu, 30 Apr 2015 11:29:48: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:29:48: # Command line: callpeak -t SRX113617.bam -f BAM -g ce -n SRX113617.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX113617.10 # format = BAM # ChIP-seq file = ['SRX113617.bam'] # control file = None # effective genome size = 9.00e+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 @ Thu, 30 Apr 2015 11:29:48: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:29:48: # Command line: callpeak -t SRX113617.bam -f BAM -g ce -n SRX113617.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX113617.20 # format = BAM # ChIP-seq file = ['SRX113617.bam'] # control file = None # effective genome size = 9.00e+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 @ Thu, 30 Apr 2015 11:29:48: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:29:48: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:29:48: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:29:48: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:29:54: 1000000 INFO @ Thu, 30 Apr 2015 11:29:54: 1000000 INFO @ Thu, 30 Apr 2015 11:29:54: 1000000 INFO @ Thu, 30 Apr 2015 11:29:59: 2000000 INFO @ Thu, 30 Apr 2015 11:29:59: 2000000 INFO @ Thu, 30 Apr 2015 11:29:59: 2000000 INFO @ Thu, 30 Apr 2015 11:30:04: 3000000 INFO @ Thu, 30 Apr 2015 11:30:04: 3000000 INFO @ Thu, 30 Apr 2015 11:30:05: 3000000 INFO @ Thu, 30 Apr 2015 11:30:10: 4000000 INFO @ Thu, 30 Apr 2015 11:30:10: 4000000 INFO @ Thu, 30 Apr 2015 11:30:10: 4000000 INFO @ Thu, 30 Apr 2015 11:30:12: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:30:12: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:30:12: #1 total tags in treatment: 4359976 INFO @ Thu, 30 Apr 2015 11:30:12: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:30:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:30:12: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:30:12: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:30:12: #1 total tags in treatment: 4359976 INFO @ Thu, 30 Apr 2015 11:30:12: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:30:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:30:12: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:30:12: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:30:12: #1 total tags in treatment: 4359976 INFO @ Thu, 30 Apr 2015 11:30:12: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:30:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:30:12: #1 tags after filtering in treatment: 4347361 INFO @ Thu, 30 Apr 2015 11:30:12: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:30:12: #1 finished! INFO @ Thu, 30 Apr 2015 11:30:12: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:30:12: #1 tags after filtering in treatment: 4347361 INFO @ Thu, 30 Apr 2015 11:30:12: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:30:12: #1 finished! INFO @ Thu, 30 Apr 2015 11:30:12: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:30:12: #1 tags after filtering in treatment: 4347361 INFO @ Thu, 30 Apr 2015 11:30:12: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:30:12: #1 finished! INFO @ Thu, 30 Apr 2015 11:30:12: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:30:14: #2 number of paired peaks: 4950 INFO @ Thu, 30 Apr 2015 11:30:14: start model_add_line... INFO @ Thu, 30 Apr 2015 11:30:14: #2 number of paired peaks: 4950 INFO @ Thu, 30 Apr 2015 11:30:14: start model_add_line... INFO @ Thu, 30 Apr 2015 11:30:14: #2 number of paired peaks: 4950 INFO @ Thu, 30 Apr 2015 11:30:14: start model_add_line... INFO @ Thu, 30 Apr 2015 11:30:35: start X-correlation... INFO @ Thu, 30 Apr 2015 11:30:35: end of X-cor INFO @ Thu, 30 Apr 2015 11:30:35: #2 finished! INFO @ Thu, 30 Apr 2015 11:30:35: #2 predicted fragment length is 164 bps INFO @ Thu, 30 Apr 2015 11:30:35: #2 alternative fragment length(s) may be 111,164,256,266,534 bps INFO @ Thu, 30 Apr 2015 11:30:35: #2.2 Generate R script for model : SRX113617.10_model.r INFO @ Thu, 30 Apr 2015 11:30:35: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:30:35: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:30:36: start X-correlation... INFO @ Thu, 30 Apr 2015 11:30:36: end of X-cor INFO @ Thu, 30 Apr 2015 11:30:36: #2 finished! INFO @ Thu, 30 Apr 2015 11:30:36: #2 predicted fragment length is 164 bps INFO @ Thu, 30 Apr 2015 11:30:36: #2 alternative fragment length(s) may be 111,164,256,266,534 bps INFO @ Thu, 30 Apr 2015 11:30:36: #2.2 Generate R script for model : SRX113617.05_model.r INFO @ Thu, 30 Apr 2015 11:30:36: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:30:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:30:36: start X-correlation... INFO @ Thu, 30 Apr 2015 11:30:36: end of X-cor INFO @ Thu, 30 Apr 2015 11:30:36: #2 finished! INFO @ Thu, 30 Apr 2015 11:30:36: #2 predicted fragment length is 164 bps INFO @ Thu, 30 Apr 2015 11:30:36: #2 alternative fragment length(s) may be 111,164,256,266,534 bps INFO @ Thu, 30 Apr 2015 11:30:36: #2.2 Generate R script for model : SRX113617.20_model.r INFO @ Thu, 30 Apr 2015 11:30:36: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:30:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:31:01: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:31:02: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:31:03: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:31:17: #4 Write output xls file... SRX113617.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:31:17: #4 Write peak in narrowPeak format file... SRX113617.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:31:17: #4 Write summits bed file... SRX113617.10_summits.bed INFO @ Thu, 30 Apr 2015 11:31:17: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (254 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:31:19: #4 Write output xls file... SRX113617.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:31:19: #4 Write peak in narrowPeak format file... SRX113617.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:31:19: #4 Write summits bed file... SRX113617.20_summits.bed INFO @ Thu, 30 Apr 2015 11:31:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (85 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:31:19: #4 Write output xls file... SRX113617.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:31:19: #4 Write peak in narrowPeak format file... SRX113617.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:31:19: #4 Write summits bed file... SRX113617.05_summits.bed INFO @ Thu, 30 Apr 2015 11:31:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (616 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。