Job ID = 8696825 sra ファイルのダウンロード中... Completed: 188973K bytes transferred in 24 seconds (62731K 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 0 0 0 0 0 0 0 0 --:--:-- 0:00:07 --:--:-- 0 100 7663 0 7663 0 0 912 0 --:--:-- 0:00:08 --:--:-- 4097 100 31492 0 31492 0 0 3335 0 --:--:-- 0:00:09 --:--:-- 10803 100 31492 0 31492 0 0 3335 0 --:--:-- 0:00:09 --:--:-- 10799 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 16846716 spots for /home/okishinya/chipatlas/results/dm3/SRX110763/SRR388345.sra Written 16846716 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:15:06 16846716 reads; of these: 16846716 (100.00%) were unpaired; of these: 2306071 (13.69%) aligned 0 times 7826149 (46.46%) aligned exactly 1 time 6714496 (39.86%) aligned >1 times 86.31% overall alignment rate Time searching: 00:15:07 Overall time: 00:15:07 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] 4283918 / 14540645 = 0.2946 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 @ Fri, 10 Mar 2017 12:20:09: # Command line: callpeak -t SRX110763.bam -f BAM -g dm -n SRX110763.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX110763.20 # format = BAM # ChIP-seq file = ['SRX110763.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 @ Fri, 10 Mar 2017 12:20:09: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:20:09: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:20:09: # Command line: callpeak -t SRX110763.bam -f BAM -g dm -n SRX110763.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX110763.10 # format = BAM # ChIP-seq file = ['SRX110763.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 @ Fri, 10 Mar 2017 12:20:09: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:20:09: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:20:09: # Command line: callpeak -t SRX110763.bam -f BAM -g dm -n SRX110763.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX110763.05 # format = BAM # ChIP-seq file = ['SRX110763.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 @ Fri, 10 Mar 2017 12:20:09: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:20:09: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:20:19: 1000000 INFO @ Fri, 10 Mar 2017 12:20:19: 1000000 INFO @ Fri, 10 Mar 2017 12:20:19: 1000000 INFO @ Fri, 10 Mar 2017 12:20:28: 2000000 INFO @ Fri, 10 Mar 2017 12:20:28: 2000000 INFO @ Fri, 10 Mar 2017 12:20:33: 2000000 INFO @ Fri, 10 Mar 2017 12:20:37: 3000000 INFO @ Fri, 10 Mar 2017 12:20:37: 3000000 INFO @ Fri, 10 Mar 2017 12:20:48: 4000000 INFO @ Fri, 10 Mar 2017 12:20:48: 4000000 INFO @ Fri, 10 Mar 2017 12:20:51: 3000000 INFO @ Fri, 10 Mar 2017 12:20:57: 5000000 INFO @ Fri, 10 Mar 2017 12:20:57: 5000000 INFO @ Fri, 10 Mar 2017 12:21:06: 4000000 INFO @ Fri, 10 Mar 2017 12:21:06: 6000000 INFO @ Fri, 10 Mar 2017 12:21:07: 6000000 INFO @ Fri, 10 Mar 2017 12:21:17: 7000000 INFO @ Fri, 10 Mar 2017 12:21:17: 7000000 INFO @ Fri, 10 Mar 2017 12:21:19: 5000000 INFO @ Fri, 10 Mar 2017 12:21:26: 8000000 INFO @ Fri, 10 Mar 2017 12:21:27: 8000000 INFO @ Fri, 10 Mar 2017 12:21:31: 6000000 INFO @ Fri, 10 Mar 2017 12:21:36: 9000000 INFO @ Fri, 10 Mar 2017 12:21:36: 9000000 INFO @ Fri, 10 Mar 2017 12:21:43: 7000000 INFO @ Fri, 10 Mar 2017 12:21:44: 10000000 INFO @ Fri, 10 Mar 2017 12:21:44: 10000000 INFO @ Fri, 10 Mar 2017 12:21:46: #1 tag size is determined as 18 bps INFO @ Fri, 10 Mar 2017 12:21:46: #1 tag size = 18 INFO @ Fri, 10 Mar 2017 12:21:46: #1 total tags in treatment: 10256727 INFO @ Fri, 10 Mar 2017 12:21:46: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:21:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:21:46: #1 tag size is determined as 18 bps INFO @ Fri, 10 Mar 2017 12:21:46: #1 tag size = 18 INFO @ Fri, 10 Mar 2017 12:21:46: #1 total tags in treatment: 10256727 INFO @ Fri, 10 Mar 2017 12:21:46: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:21:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:21:48: #1 tags after filtering in treatment: 10256727 INFO @ Fri, 10 Mar 2017 12:21:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:21:48: #1 finished! INFO @ Fri, 10 Mar 2017 12:21:48: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:21:48: #1 tags after filtering in treatment: 10256727 INFO @ Fri, 10 Mar 2017 12:21:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:21:48: #1 finished! INFO @ Fri, 10 Mar 2017 12:21:48: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:21:51: #2 number of paired peaks: 3366 INFO @ Fri, 10 Mar 2017 12:21:51: start model_add_line... INFO @ Fri, 10 Mar 2017 12:21:51: #2 number of paired peaks: 3366 INFO @ Fri, 10 Mar 2017 12:21:51: start model_add_line... INFO @ Fri, 10 Mar 2017 12:21:56: 8000000 INFO @ Fri, 10 Mar 2017 12:22:09: 9000000 INFO @ Fri, 10 Mar 2017 12:22:20: start X-correlation... INFO @ Fri, 10 Mar 2017 12:22:20: end of X-cor INFO @ Fri, 10 Mar 2017 12:22:20: #2 finished! INFO @ Fri, 10 Mar 2017 12:22:20: #2 predicted fragment length is 87 bps INFO @ Fri, 10 Mar 2017 12:22:20: #2 alternative fragment length(s) may be 87 bps INFO @ Fri, 10 Mar 2017 12:22:20: #2.2 Generate R script for model : SRX110763.10_model.r INFO @ Fri, 10 Mar 2017 12:22:20: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:22:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:22:20: start X-correlation... INFO @ Fri, 10 Mar 2017 12:22:20: end of X-cor INFO @ Fri, 10 Mar 2017 12:22:20: #2 finished! INFO @ Fri, 10 Mar 2017 12:22:20: #2 predicted fragment length is 87 bps INFO @ Fri, 10 Mar 2017 12:22:20: #2 alternative fragment length(s) may be 87 bps INFO @ Fri, 10 Mar 2017 12:22:20: #2.2 Generate R script for model : SRX110763.05_model.r INFO @ Fri, 10 Mar 2017 12:22:20: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:22:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:22:21: 10000000 INFO @ Fri, 10 Mar 2017 12:22:24: #1 tag size is determined as 18 bps INFO @ Fri, 10 Mar 2017 12:22:24: #1 tag size = 18 INFO @ Fri, 10 Mar 2017 12:22:24: #1 total tags in treatment: 10256727 INFO @ Fri, 10 Mar 2017 12:22:24: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:22:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:22:26: #1 tags after filtering in treatment: 10256727 INFO @ Fri, 10 Mar 2017 12:22:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:22:26: #1 finished! INFO @ Fri, 10 Mar 2017 12:22:26: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:22:29: #2 number of paired peaks: 3366 INFO @ Fri, 10 Mar 2017 12:22:29: start model_add_line... INFO @ Fri, 10 Mar 2017 12:22:59: start X-correlation... INFO @ Fri, 10 Mar 2017 12:22:59: end of X-cor INFO @ Fri, 10 Mar 2017 12:22:59: #2 finished! INFO @ Fri, 10 Mar 2017 12:22:59: #2 predicted fragment length is 87 bps INFO @ Fri, 10 Mar 2017 12:22:59: #2 alternative fragment length(s) may be 87 bps INFO @ Fri, 10 Mar 2017 12:22:59: #2.2 Generate R script for model : SRX110763.20_model.r INFO @ Fri, 10 Mar 2017 12:22:59: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:22:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:23:30: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:23:34: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:24:13: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:24:28: #4 Write output xls file... SRX110763.10_peaks.xls INFO @ Fri, 10 Mar 2017 12:24:28: #4 Write peak in narrowPeak format file... SRX110763.10_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:24:28: #4 Write summits bed file... SRX110763.10_summits.bed INFO @ Fri, 10 Mar 2017 12:24:28: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (6777 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 12:24:34: #4 Write output xls file... SRX110763.05_peaks.xls INFO @ Fri, 10 Mar 2017 12:24:34: #4 Write peak in narrowPeak format file... SRX110763.05_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:24:35: #4 Write summits bed file... SRX110763.05_summits.bed INFO @ Fri, 10 Mar 2017 12:24:35: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (8861 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 12:25:11: #4 Write output xls file... SRX110763.20_peaks.xls INFO @ Fri, 10 Mar 2017 12:25:11: #4 Write peak in narrowPeak format file... SRX110763.20_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:25:11: #4 Write summits bed file... SRX110763.20_summits.bed INFO @ Fri, 10 Mar 2017 12:25:11: Done! pass1 - making usageList (14 chroms): 8 millis pass2 - checking and writing primary data (4779 records, 4 fields): 36 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。