Job ID = 9028928 sra ファイルのダウンロード中... Completed: 387610K bytes transferred in 6 seconds (454126K 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 --:--:-- 0:00:06 --:--:-- 0 100 22318 0 22318 0 0 2839 0 --:--:-- 0:00:07 --:--:-- 17354 100 46318 0 46318 0 0 5408 0 --:--:-- 0:00:08 --:--:-- 23263 100 66567 0 66567 0 0 7516 0 --:--:-- 0:00:08 --:--:-- 29170 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 9781054 spots for /home/okishinya/chipatlas/results/dm3/SRX1038029/SRR2039658.sra Written 9781054 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: 00:01:13 9781054 reads; of these: 9781054 (100.00%) were unpaired; of these: 7564155 (77.33%) aligned 0 times 2003910 (20.49%) aligned exactly 1 time 212989 (2.18%) aligned >1 times 22.67% overall alignment rate Time searching: 00:01:13 Overall time: 00:01:13 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 418122 / 2216899 = 0.1886 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 @ Sat, 03 Jun 2017 12:26:27: # Command line: callpeak -t SRX1038029.bam -f BAM -g dm -n SRX1038029.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1038029.10 # format = BAM # ChIP-seq file = ['SRX1038029.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sat, 03 Jun 2017 12:26:27: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:26:27: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:26:27: # Command line: callpeak -t SRX1038029.bam -f BAM -g dm -n SRX1038029.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1038029.05 # format = BAM # ChIP-seq file = ['SRX1038029.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sat, 03 Jun 2017 12:26:27: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:26:27: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:26:27: # Command line: callpeak -t SRX1038029.bam -f BAM -g dm -n SRX1038029.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1038029.20 # format = BAM # ChIP-seq file = ['SRX1038029.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sat, 03 Jun 2017 12:26:27: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:26:27: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:26:34: 1000000 INFO @ Sat, 03 Jun 2017 12:26:34: 1000000 INFO @ Sat, 03 Jun 2017 12:26:34: 1000000 INFO @ Sat, 03 Jun 2017 12:26:40: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 12:26:40: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 12:26:40: #1 total tags in treatment: 1798777 INFO @ Sat, 03 Jun 2017 12:26:40: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:26:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 12:26:40: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 12:26:40: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 12:26:40: #1 total tags in treatment: 1798777 INFO @ Sat, 03 Jun 2017 12:26:40: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:26:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 12:26:40: #1 tags after filtering in treatment: 1797980 INFO @ Sat, 03 Jun 2017 12:26:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:26:40: #1 finished! INFO @ Sat, 03 Jun 2017 12:26:40: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:26:41: #1 tags after filtering in treatment: 1797980 INFO @ Sat, 03 Jun 2017 12:26:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:26:41: #1 finished! INFO @ Sat, 03 Jun 2017 12:26:41: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:26:41: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 12:26:41: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 12:26:41: #1 total tags in treatment: 1798777 INFO @ Sat, 03 Jun 2017 12:26:41: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:26:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 12:26:41: #1 tags after filtering in treatment: 1797980 INFO @ Sat, 03 Jun 2017 12:26:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:26:41: #1 finished! INFO @ Sat, 03 Jun 2017 12:26:41: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:26:41: #2 number of paired peaks: 4879 INFO @ Sat, 03 Jun 2017 12:26:41: start model_add_line... INFO @ Sat, 03 Jun 2017 12:26:41: #2 number of paired peaks: 4879 INFO @ Sat, 03 Jun 2017 12:26:41: start model_add_line... INFO @ Sat, 03 Jun 2017 12:26:42: #2 number of paired peaks: 4879 INFO @ Sat, 03 Jun 2017 12:26:42: start model_add_line... INFO @ Sat, 03 Jun 2017 12:26:51: start X-correlation... INFO @ Sat, 03 Jun 2017 12:26:51: end of X-cor INFO @ Sat, 03 Jun 2017 12:26:51: #2 finished! INFO @ Sat, 03 Jun 2017 12:26:51: #2 predicted fragment length is 153 bps INFO @ Sat, 03 Jun 2017 12:26:51: #2 alternative fragment length(s) may be 153 bps INFO @ Sat, 03 Jun 2017 12:26:51: #2.2 Generate R script for model : SRX1038029.10_model.r INFO @ Sat, 03 Jun 2017 12:26:51: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:26:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:26:51: start X-correlation... INFO @ Sat, 03 Jun 2017 12:26:51: end of X-cor INFO @ Sat, 03 Jun 2017 12:26:51: #2 finished! INFO @ Sat, 03 Jun 2017 12:26:51: #2 predicted fragment length is 153 bps INFO @ Sat, 03 Jun 2017 12:26:51: #2 alternative fragment length(s) may be 153 bps INFO @ Sat, 03 Jun 2017 12:26:51: #2.2 Generate R script for model : SRX1038029.05_model.r INFO @ Sat, 03 Jun 2017 12:26:51: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:26:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:26:52: start X-correlation... INFO @ Sat, 03 Jun 2017 12:26:52: end of X-cor INFO @ Sat, 03 Jun 2017 12:26:52: #2 finished! INFO @ Sat, 03 Jun 2017 12:26:52: #2 predicted fragment length is 153 bps INFO @ Sat, 03 Jun 2017 12:26:52: #2 alternative fragment length(s) may be 153 bps INFO @ Sat, 03 Jun 2017 12:26:52: #2.2 Generate R script for model : SRX1038029.20_model.r INFO @ Sat, 03 Jun 2017 12:26:52: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:26:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:27:03: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:27:04: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:27:05: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 03 Jun 2017 12:27:12: #4 Write output xls file... SRX1038029.10_peaks.xls INFO @ Sat, 03 Jun 2017 12:27:12: #4 Write peak in narrowPeak format file... SRX1038029.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:27:12: #4 Write summits bed file... SRX1038029.10_summits.bed INFO @ Sat, 03 Jun 2017 12:27:12: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1116 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:27:13: #4 Write output xls file... SRX1038029.05_peaks.xls INFO @ Sat, 03 Jun 2017 12:27:13: #4 Write peak in narrowPeak format file... SRX1038029.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:27:13: #4 Write summits bed file... SRX1038029.05_summits.bed INFO @ Sat, 03 Jun 2017 12:27:13: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1927 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:27:13: #4 Write output xls file... SRX1038029.20_peaks.xls INFO @ Sat, 03 Jun 2017 12:27:13: #4 Write peak in narrowPeak format file... SRX1038029.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:27:13: #4 Write summits bed file... SRX1038029.20_summits.bed INFO @ Sat, 03 Jun 2017 12:27:13: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (671 records, 4 fields): 2 millis CompletedMACS2peakCalling