Job ID = 2236891 sra ファイルのダウンロード中... Completed: 429987K bytes transferred in 10 seconds (330060K 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 16373 0 16373 0 0 22567 0 --:--:-- --:--:-- --:--:-- 30661 100 35253 0 35253 0 0 48534 0 --:--:-- --:--:-- --:--:-- 66016 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 21006018 spots for /home/okishinya/chipatlas/results/ce10/SRX059273/SRR190713.sra Written 21006018 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: 00:03:09 21006018 reads; of these: 21006018 (100.00%) were unpaired; of these: 7277930 (34.65%) aligned 0 times 12187059 (58.02%) aligned exactly 1 time 1541029 (7.34%) aligned >1 times 65.35% overall alignment rate Time searching: 00:03:09 Overall time: 00:03:09 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] 3459961 / 13728088 = 0.2520 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 11:18:17: # Command line: callpeak -t SRX059273.bam -f BAM -g ce -n SRX059273.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX059273.10 # format = BAM # ChIP-seq file = ['SRX059273.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 11:18:17: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:18:17: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:18:17: # Command line: callpeak -t SRX059273.bam -f BAM -g ce -n SRX059273.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX059273.20 # format = BAM # ChIP-seq file = ['SRX059273.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 11:18:17: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:18:17: # Command line: callpeak -t SRX059273.bam -f BAM -g ce -n SRX059273.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX059273.05 # format = BAM # ChIP-seq file = ['SRX059273.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 11:18:17: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:18:17: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:18:17: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:18:23: 1000000 INFO @ Thu, 30 Apr 2015 11:18:23: 1000000 INFO @ Thu, 30 Apr 2015 11:18:23: 1000000 INFO @ Thu, 30 Apr 2015 11:18:28: 2000000 INFO @ Thu, 30 Apr 2015 11:18:28: 2000000 INFO @ Thu, 30 Apr 2015 11:18:28: 2000000 INFO @ Thu, 30 Apr 2015 11:18:33: 3000000 INFO @ Thu, 30 Apr 2015 11:18:33: 3000000 INFO @ Thu, 30 Apr 2015 11:18:33: 3000000 INFO @ Thu, 30 Apr 2015 11:18:38: 4000000 INFO @ Thu, 30 Apr 2015 11:18:39: 4000000 INFO @ Thu, 30 Apr 2015 11:18:39: 4000000 INFO @ Thu, 30 Apr 2015 11:18:44: 5000000 INFO @ Thu, 30 Apr 2015 11:18:44: 5000000 INFO @ Thu, 30 Apr 2015 11:18:45: 5000000 INFO @ Thu, 30 Apr 2015 11:18:49: 6000000 INFO @ Thu, 30 Apr 2015 11:18:49: 6000000 INFO @ Thu, 30 Apr 2015 11:18:52: 6000000 INFO @ Thu, 30 Apr 2015 11:18:54: 7000000 INFO @ Thu, 30 Apr 2015 11:18:54: 7000000 INFO @ Thu, 30 Apr 2015 11:18:57: 7000000 INFO @ Thu, 30 Apr 2015 11:18:59: 8000000 INFO @ Thu, 30 Apr 2015 11:19:00: 8000000 INFO @ Thu, 30 Apr 2015 11:19:02: 8000000 INFO @ Thu, 30 Apr 2015 11:19:05: 9000000 INFO @ Thu, 30 Apr 2015 11:19:05: 9000000 INFO @ Thu, 30 Apr 2015 11:19:07: 9000000 INFO @ Thu, 30 Apr 2015 11:19:10: 10000000 INFO @ Thu, 30 Apr 2015 11:19:10: 10000000 INFO @ Thu, 30 Apr 2015 11:19:12: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:19:12: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:19:12: #1 total tags in treatment: 10268127 INFO @ Thu, 30 Apr 2015 11:19:12: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:19:12: #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 11:19:12: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:19:12: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:19:12: #1 total tags in treatment: 10268127 INFO @ Thu, 30 Apr 2015 11:19:12: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:19:12: #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 11:19:12: 10000000 INFO @ Thu, 30 Apr 2015 11:19:13: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:19:13: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:19:13: #1 total tags in treatment: 10268127 INFO @ Thu, 30 Apr 2015 11:19:13: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:19:13: #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 11:19:13: #1 tags after filtering in treatment: 10267361 INFO @ Thu, 30 Apr 2015 11:19:13: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:19:13: #1 finished! INFO @ Thu, 30 Apr 2015 11:19:13: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:19:14: #1 tags after filtering in treatment: 10267361 INFO @ Thu, 30 Apr 2015 11:19:14: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:19:14: #1 finished! INFO @ Thu, 30 Apr 2015 11:19:14: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:19:15: #1 tags after filtering in treatment: 10267361 INFO @ Thu, 30 Apr 2015 11:19:15: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:19:15: #1 finished! INFO @ Thu, 30 Apr 2015 11:19:15: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:19:16: #2 number of paired peaks: 3949 INFO @ Thu, 30 Apr 2015 11:19:16: start model_add_line... INFO @ Thu, 30 Apr 2015 11:19:16: #2 number of paired peaks: 3949 INFO @ Thu, 30 Apr 2015 11:19:16: start model_add_line... INFO @ Thu, 30 Apr 2015 11:19:18: #2 number of paired peaks: 3949 INFO @ Thu, 30 Apr 2015 11:19:18: start model_add_line... INFO @ Thu, 30 Apr 2015 11:19:51: start X-correlation... INFO @ Thu, 30 Apr 2015 11:19:51: end of X-cor INFO @ Thu, 30 Apr 2015 11:19:51: #2 finished! INFO @ Thu, 30 Apr 2015 11:19:51: #2 predicted fragment length is 233 bps INFO @ Thu, 30 Apr 2015 11:19:51: #2 alternative fragment length(s) may be 233 bps INFO @ Thu, 30 Apr 2015 11:19:51: #2.2 Generate R script for model : SRX059273.05_model.r INFO @ Thu, 30 Apr 2015 11:19:51: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:19:51: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:19:52: start X-correlation... INFO @ Thu, 30 Apr 2015 11:19:52: end of X-cor INFO @ Thu, 30 Apr 2015 11:19:52: #2 finished! INFO @ Thu, 30 Apr 2015 11:19:52: #2 predicted fragment length is 233 bps INFO @ Thu, 30 Apr 2015 11:19:52: #2 alternative fragment length(s) may be 233 bps INFO @ Thu, 30 Apr 2015 11:19:52: #2.2 Generate R script for model : SRX059273.20_model.r INFO @ Thu, 30 Apr 2015 11:19:52: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:19:52: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:19:53: start X-correlation... INFO @ Thu, 30 Apr 2015 11:19:53: end of X-cor INFO @ Thu, 30 Apr 2015 11:19:53: #2 finished! INFO @ Thu, 30 Apr 2015 11:19:53: #2 predicted fragment length is 233 bps INFO @ Thu, 30 Apr 2015 11:19:53: #2 alternative fragment length(s) may be 233 bps INFO @ Thu, 30 Apr 2015 11:19:53: #2.2 Generate R script for model : SRX059273.10_model.r INFO @ Thu, 30 Apr 2015 11:19:53: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:19:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:20:57: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:21:00: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:21:01: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:21:45: #4 Write output xls file... SRX059273.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:21:45: #4 Write peak in narrowPeak format file... SRX059273.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:21:46: #4 Write summits bed file... SRX059273.20_summits.bed INFO @ Thu, 30 Apr 2015 11:21:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3511 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:21:52: #4 Write output xls file... SRX059273.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:21:53: #4 Write peak in narrowPeak format file... SRX059273.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:21:53: #4 Write summits bed file... SRX059273.05_summits.bed INFO @ Thu, 30 Apr 2015 11:21:53: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5240 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:21:55: #4 Write output xls file... SRX059273.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:21:55: #4 Write peak in narrowPeak format file... SRX059273.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:21:55: #4 Write summits bed file... SRX059273.10_summits.bed INFO @ Thu, 30 Apr 2015 11:21:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4289 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。