Job ID = 9029321 sra ファイルのダウンロード中... Completed: 140077K bytes transferred in 4 seconds (262631K 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 12695 0 12695 0 0 1707 0 --:--:-- 0:00:07 --:--:-- 12385 100 46318 0 46318 0 0 5494 0 --:--:-- 0:00:08 --:--:-- 22918 100 64585 0 64585 0 0 7371 0 --:--:-- 0:00:08 --:--:-- 27447 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 4532862 spots for /home/okishinya/chipatlas/results/dm3/SRX1561063/SRR3145065.sra Written 4532862 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: 00:01:14 4532862 reads; of these: 4532862 (100.00%) were unpaired; of these: 735079 (16.22%) aligned 0 times 3354696 (74.01%) aligned exactly 1 time 443087 (9.77%) aligned >1 times 83.78% overall alignment rate Time searching: 00:01:14 Overall time: 00:01:14 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] 871293 / 3797783 = 0.2294 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 13:14:24: # Command line: callpeak -t SRX1561063.bam -f BAM -g dm -n SRX1561063.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1561063.05 # format = BAM # ChIP-seq file = ['SRX1561063.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 13:14:24: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:14:24: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:14:24: # Command line: callpeak -t SRX1561063.bam -f BAM -g dm -n SRX1561063.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1561063.20 # format = BAM # ChIP-seq file = ['SRX1561063.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 13:14:24: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:14:24: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:14:24: # Command line: callpeak -t SRX1561063.bam -f BAM -g dm -n SRX1561063.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1561063.10 # format = BAM # ChIP-seq file = ['SRX1561063.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 13:14:24: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:14:24: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:14:31: 1000000 INFO @ Sat, 03 Jun 2017 13:14:31: 1000000 INFO @ Sat, 03 Jun 2017 13:14:31: 1000000 INFO @ Sat, 03 Jun 2017 13:14:38: 2000000 INFO @ Sat, 03 Jun 2017 13:14:38: 2000000 INFO @ Sat, 03 Jun 2017 13:14:40: 2000000 INFO @ Sat, 03 Jun 2017 13:14:45: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:14:45: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:14:45: #1 total tags in treatment: 2926490 INFO @ Sat, 03 Jun 2017 13:14:45: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:14:45: #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 13:14:45: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:14:45: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:14:45: #1 total tags in treatment: 2926490 INFO @ Sat, 03 Jun 2017 13:14:45: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:14:45: #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 13:14:45: #1 tags after filtering in treatment: 2925459 INFO @ Sat, 03 Jun 2017 13:14:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:14:45: #1 finished! INFO @ Sat, 03 Jun 2017 13:14:45: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:14:45: #1 tags after filtering in treatment: 2925459 INFO @ Sat, 03 Jun 2017 13:14:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:14:45: #1 finished! INFO @ Sat, 03 Jun 2017 13:14:45: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:14:46: #2 number of paired peaks: 3826 INFO @ Sat, 03 Jun 2017 13:14:46: start model_add_line... INFO @ Sat, 03 Jun 2017 13:14:46: #2 number of paired peaks: 3826 INFO @ Sat, 03 Jun 2017 13:14:46: start model_add_line... INFO @ Sat, 03 Jun 2017 13:14:47: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:14:47: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:14:47: #1 total tags in treatment: 2926490 INFO @ Sat, 03 Jun 2017 13:14:47: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:14:47: #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 13:14:47: #1 tags after filtering in treatment: 2925459 INFO @ Sat, 03 Jun 2017 13:14:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:14:47: #1 finished! INFO @ Sat, 03 Jun 2017 13:14:47: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:14:48: #2 number of paired peaks: 3826 INFO @ Sat, 03 Jun 2017 13:14:48: start model_add_line... INFO @ Sat, 03 Jun 2017 13:14:54: start X-correlation... INFO @ Sat, 03 Jun 2017 13:14:54: end of X-cor INFO @ Sat, 03 Jun 2017 13:14:54: #2 finished! INFO @ Sat, 03 Jun 2017 13:14:54: #2 predicted fragment length is 153 bps INFO @ Sat, 03 Jun 2017 13:14:54: #2 alternative fragment length(s) may be 153 bps INFO @ Sat, 03 Jun 2017 13:14:54: #2.2 Generate R script for model : SRX1561063.05_model.r INFO @ Sat, 03 Jun 2017 13:14:54: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:14:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:14:55: start X-correlation... INFO @ Sat, 03 Jun 2017 13:14:55: end of X-cor INFO @ Sat, 03 Jun 2017 13:14:55: #2 finished! INFO @ Sat, 03 Jun 2017 13:14:55: #2 predicted fragment length is 153 bps INFO @ Sat, 03 Jun 2017 13:14:55: #2 alternative fragment length(s) may be 153 bps INFO @ Sat, 03 Jun 2017 13:14:55: #2.2 Generate R script for model : SRX1561063.10_model.r INFO @ Sat, 03 Jun 2017 13:14:55: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:14:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:14:57: start X-correlation... INFO @ Sat, 03 Jun 2017 13:14:57: end of X-cor INFO @ Sat, 03 Jun 2017 13:14:57: #2 finished! INFO @ Sat, 03 Jun 2017 13:14:57: #2 predicted fragment length is 153 bps INFO @ Sat, 03 Jun 2017 13:14:57: #2 alternative fragment length(s) may be 153 bps INFO @ Sat, 03 Jun 2017 13:14:57: #2.2 Generate R script for model : SRX1561063.20_model.r INFO @ Sat, 03 Jun 2017 13:14:57: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:14:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:15:14: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:15:14: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:15:18: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:15:30: #4 Write output xls file... SRX1561063.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:15:30: #4 Write peak in narrowPeak format file... SRX1561063.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:15:30: #4 Write summits bed file... SRX1561063.10_summits.bed INFO @ Sat, 03 Jun 2017 13:15:30: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (3604 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Jun 2017 13:15:32: #4 Write output xls file... SRX1561063.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:15:32: #4 Write peak in narrowPeak format file... SRX1561063.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:15:32: #4 Write summits bed file... SRX1561063.05_summits.bed INFO @ Sat, 03 Jun 2017 13:15:32: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (5775 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:15:34: #4 Write output xls file... SRX1561063.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:15:34: #4 Write peak in narrowPeak format file... SRX1561063.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:15:34: #4 Write summits bed file... SRX1561063.20_summits.bed INFO @ Sat, 03 Jun 2017 13:15:34: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (2002 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。