Job ID = 2162399 sra ファイルのダウンロード中... Completed: 1136824K bytes transferred in 11 seconds (780054K 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 36536 0 36536 0 0 49892 0 --:--:-- --:--:-- --:--:-- 67534 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 55245827 spots for /home/okishinya/chipatlas/results/dm3/SRX084581/SRR315121.sra Written 55245827 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:13:35 55245827 reads; of these: 55245827 (100.00%) were unpaired; of these: 17932879 (32.46%) aligned 0 times 26687523 (48.31%) aligned exactly 1 time 10625425 (19.23%) aligned >1 times 67.54% overall alignment rate Time searching: 00:13:36 Overall time: 00:13:36 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_sort_core] merging from 12 files... [bam_rmdupse_core] 17596652 / 37312948 = 0.4716 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 @ Tue, 21 Apr 2015 14:09:07: # Command line: callpeak -t SRX084581.bam -f BAM -g dm -n SRX084581.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX084581.20 # format = BAM # ChIP-seq file = ['SRX084581.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 @ Tue, 21 Apr 2015 14:09:07: # Command line: callpeak -t SRX084581.bam -f BAM -g dm -n SRX084581.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX084581.10 # format = BAM # ChIP-seq file = ['SRX084581.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 @ Tue, 21 Apr 2015 14:09:07: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:09:07: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:09:07: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:09:07: # Command line: callpeak -t SRX084581.bam -f BAM -g dm -n SRX084581.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX084581.05 # format = BAM # ChIP-seq file = ['SRX084581.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 @ Tue, 21 Apr 2015 14:09:07: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:09:07: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:09:07: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:09:14: 1000000 INFO @ Tue, 21 Apr 2015 14:09:14: 1000000 INFO @ Tue, 21 Apr 2015 14:09:14: 1000000 INFO @ Tue, 21 Apr 2015 14:09:20: 2000000 INFO @ Tue, 21 Apr 2015 14:09:20: 2000000 INFO @ Tue, 21 Apr 2015 14:09:20: 2000000 INFO @ Tue, 21 Apr 2015 14:09:26: 3000000 INFO @ Tue, 21 Apr 2015 14:09:26: 3000000 INFO @ Tue, 21 Apr 2015 14:09:26: 3000000 INFO @ Tue, 21 Apr 2015 14:09:32: 4000000 INFO @ Tue, 21 Apr 2015 14:09:32: 4000000 INFO @ Tue, 21 Apr 2015 14:09:32: 4000000 INFO @ Tue, 21 Apr 2015 14:09:38: 5000000 INFO @ Tue, 21 Apr 2015 14:09:38: 5000000 INFO @ Tue, 21 Apr 2015 14:09:38: 5000000 INFO @ Tue, 21 Apr 2015 14:09:44: 6000000 INFO @ Tue, 21 Apr 2015 14:09:44: 6000000 INFO @ Tue, 21 Apr 2015 14:09:44: 6000000 INFO @ Tue, 21 Apr 2015 14:09:50: 7000000 INFO @ Tue, 21 Apr 2015 14:09:50: 7000000 INFO @ Tue, 21 Apr 2015 14:09:50: 7000000 INFO @ Tue, 21 Apr 2015 14:09:56: 8000000 INFO @ Tue, 21 Apr 2015 14:09:56: 8000000 INFO @ Tue, 21 Apr 2015 14:09:56: 8000000 INFO @ Tue, 21 Apr 2015 14:10:01: 9000000 INFO @ Tue, 21 Apr 2015 14:10:02: 9000000 INFO @ Tue, 21 Apr 2015 14:10:02: 9000000 INFO @ Tue, 21 Apr 2015 14:10:07: 10000000 INFO @ Tue, 21 Apr 2015 14:10:07: 10000000 INFO @ Tue, 21 Apr 2015 14:10:07: 10000000 INFO @ Tue, 21 Apr 2015 14:10:13: 11000000 INFO @ Tue, 21 Apr 2015 14:10:13: 11000000 INFO @ Tue, 21 Apr 2015 14:10:13: 11000000 INFO @ Tue, 21 Apr 2015 14:10:19: 12000000 INFO @ Tue, 21 Apr 2015 14:10:19: 12000000 INFO @ Tue, 21 Apr 2015 14:10:19: 12000000 INFO @ Tue, 21 Apr 2015 14:10:24: 13000000 INFO @ Tue, 21 Apr 2015 14:10:25: 13000000 INFO @ Tue, 21 Apr 2015 14:10:25: 13000000 INFO @ Tue, 21 Apr 2015 14:10:30: 14000000 INFO @ Tue, 21 Apr 2015 14:10:31: 14000000 INFO @ Tue, 21 Apr 2015 14:10:31: 14000000 INFO @ Tue, 21 Apr 2015 14:10:36: 15000000 INFO @ Tue, 21 Apr 2015 14:10:36: 15000000 INFO @ Tue, 21 Apr 2015 14:10:36: 15000000 INFO @ Tue, 21 Apr 2015 14:10:42: 16000000 INFO @ Tue, 21 Apr 2015 14:10:42: 16000000 INFO @ Tue, 21 Apr 2015 14:10:42: 16000000 INFO @ Tue, 21 Apr 2015 14:10:47: 17000000 INFO @ Tue, 21 Apr 2015 14:10:48: 17000000 INFO @ Tue, 21 Apr 2015 14:10:48: 17000000 INFO @ Tue, 21 Apr 2015 14:10:53: 18000000 INFO @ Tue, 21 Apr 2015 14:10:54: 18000000 INFO @ Tue, 21 Apr 2015 14:10:54: 18000000 INFO @ Tue, 21 Apr 2015 14:10:59: 19000000 INFO @ Tue, 21 Apr 2015 14:10:59: 19000000 INFO @ Tue, 21 Apr 2015 14:10:59: 19000000 INFO @ Tue, 21 Apr 2015 14:11:03: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 14:11:03: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 14:11:03: #1 total tags in treatment: 19716296 INFO @ Tue, 21 Apr 2015 14:11:03: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:11:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 14:11:04: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 14:11:04: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 14:11:04: #1 total tags in treatment: 19716296 INFO @ Tue, 21 Apr 2015 14:11:04: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:11:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 14:11:04: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 14:11:04: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 14:11:04: #1 total tags in treatment: 19716296 INFO @ Tue, 21 Apr 2015 14:11:04: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:11:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 14:11:07: #1 tags after filtering in treatment: 19709373 INFO @ Tue, 21 Apr 2015 14:11:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:11:07: #1 finished! INFO @ Tue, 21 Apr 2015 14:11:07: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:11:07: #1 tags after filtering in treatment: 19709373 INFO @ Tue, 21 Apr 2015 14:11:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:11:07: #1 finished! INFO @ Tue, 21 Apr 2015 14:11:07: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:11:07: #1 tags after filtering in treatment: 19709373 INFO @ Tue, 21 Apr 2015 14:11:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:11:07: #1 finished! INFO @ Tue, 21 Apr 2015 14:11:07: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:11:10: #2 number of paired peaks: 2732 INFO @ Tue, 21 Apr 2015 14:11:10: start model_add_line... INFO @ Tue, 21 Apr 2015 14:11:11: #2 number of paired peaks: 2732 INFO @ Tue, 21 Apr 2015 14:11:11: start model_add_line... INFO @ Tue, 21 Apr 2015 14:11:11: #2 number of paired peaks: 2732 INFO @ Tue, 21 Apr 2015 14:11:11: start model_add_line... INFO @ Tue, 21 Apr 2015 14:11:43: start X-correlation... INFO @ Tue, 21 Apr 2015 14:11:43: end of X-cor INFO @ Tue, 21 Apr 2015 14:11:43: #2 finished! INFO @ Tue, 21 Apr 2015 14:11:43: #2 predicted fragment length is 75 bps INFO @ Tue, 21 Apr 2015 14:11:43: #2 alternative fragment length(s) may be 4,75 bps INFO @ Tue, 21 Apr 2015 14:11:43: #2.2 Generate R script for model : SRX084581.20_model.r INFO @ Tue, 21 Apr 2015 14:11:43: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:11:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:11:44: start X-correlation... INFO @ Tue, 21 Apr 2015 14:11:44: end of X-cor INFO @ Tue, 21 Apr 2015 14:11:44: #2 finished! INFO @ Tue, 21 Apr 2015 14:11:44: #2 predicted fragment length is 75 bps INFO @ Tue, 21 Apr 2015 14:11:44: #2 alternative fragment length(s) may be 4,75 bps INFO @ Tue, 21 Apr 2015 14:11:44: #2.2 Generate R script for model : SRX084581.05_model.r INFO @ Tue, 21 Apr 2015 14:11:44: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:11:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:11:44: start X-correlation... INFO @ Tue, 21 Apr 2015 14:11:44: end of X-cor INFO @ Tue, 21 Apr 2015 14:11:44: #2 finished! INFO @ Tue, 21 Apr 2015 14:11:44: #2 predicted fragment length is 75 bps INFO @ Tue, 21 Apr 2015 14:11:44: #2 alternative fragment length(s) may be 4,75 bps INFO @ Tue, 21 Apr 2015 14:11:44: #2.2 Generate R script for model : SRX084581.10_model.r INFO @ Tue, 21 Apr 2015 14:11:44: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:11:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:13:19: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:13:24: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:13:25: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:14:30: #4 Write output xls file... SRX084581.20_peaks.xls INFO @ Tue, 21 Apr 2015 14:14:30: #4 Write peak in narrowPeak format file... SRX084581.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:14:30: #4 Write summits bed file... SRX084581.20_summits.bed INFO @ Tue, 21 Apr 2015 14:14:30: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5443 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:14:44: #4 Write output xls file... SRX084581.10_peaks.xls INFO @ Tue, 21 Apr 2015 14:14:44: #4 Write peak in narrowPeak format file... SRX084581.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:14:44: #4 Write summits bed file... SRX084581.10_summits.bed INFO @ Tue, 21 Apr 2015 14:14:44: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (10935 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:14:45: #4 Write output xls file... SRX084581.05_peaks.xls INFO @ Tue, 21 Apr 2015 14:14:45: #4 Write peak in narrowPeak format file... SRX084581.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:14:45: #4 Write summits bed file... SRX084581.05_summits.bed INFO @ Tue, 21 Apr 2015 14:14:45: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (17891 records, 4 fields): 21 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。