Job ID = 2161329 sra ファイルのダウンロード中... Completed: 448701K bytes transferred in 6 seconds (547620K 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 4000 0 4000 0 0 7386 0 --:--:-- --:--:-- --:--:-- 11396 100 37990 0 37990 0 0 51915 0 --:--:-- --:--:-- --:--:-- 70221 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 15205289 spots for /home/okishinya/chipatlas/results/dm3/SRX018160/SRR038617.sra Written 15205289 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: 00:03:36 15205289 reads; of these: 15205289 (100.00%) were unpaired; of these: 5405563 (35.55%) aligned 0 times 6849959 (45.05%) aligned exactly 1 time 2949767 (19.40%) aligned >1 times 64.45% overall alignment rate Time searching: 00:03:36 Overall time: 00:03:36 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_rmdupse_core] 2032625 / 9799726 = 0.2074 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 12:28:42: # Command line: callpeak -t SRX018160.bam -f BAM -g dm -n SRX018160.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX018160.20 # format = BAM # ChIP-seq file = ['SRX018160.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 12:28:42: # Command line: callpeak -t SRX018160.bam -f BAM -g dm -n SRX018160.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX018160.05 # format = BAM # ChIP-seq file = ['SRX018160.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 12:28:42: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:28:42: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:28:42: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:28:42: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:28:42: # Command line: callpeak -t SRX018160.bam -f BAM -g dm -n SRX018160.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX018160.10 # format = BAM # ChIP-seq file = ['SRX018160.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 12:28:42: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:28:42: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:28:47: 1000000 INFO @ Tue, 21 Apr 2015 12:28:47: 1000000 INFO @ Tue, 21 Apr 2015 12:28:47: 1000000 INFO @ Tue, 21 Apr 2015 12:28:52: 2000000 INFO @ Tue, 21 Apr 2015 12:28:52: 2000000 INFO @ Tue, 21 Apr 2015 12:28:52: 2000000 INFO @ Tue, 21 Apr 2015 12:28:57: 3000000 INFO @ Tue, 21 Apr 2015 12:28:58: 3000000 INFO @ Tue, 21 Apr 2015 12:28:58: 3000000 INFO @ Tue, 21 Apr 2015 12:29:03: 4000000 INFO @ Tue, 21 Apr 2015 12:29:03: 4000000 INFO @ Tue, 21 Apr 2015 12:29:03: 4000000 INFO @ Tue, 21 Apr 2015 12:29:08: 5000000 INFO @ Tue, 21 Apr 2015 12:29:08: 5000000 INFO @ Tue, 21 Apr 2015 12:29:09: 5000000 INFO @ Tue, 21 Apr 2015 12:29:13: 6000000 INFO @ Tue, 21 Apr 2015 12:29:14: 6000000 INFO @ Tue, 21 Apr 2015 12:29:14: 6000000 INFO @ Tue, 21 Apr 2015 12:29:19: 7000000 INFO @ Tue, 21 Apr 2015 12:29:19: 7000000 INFO @ Tue, 21 Apr 2015 12:29:20: 7000000 INFO @ Tue, 21 Apr 2015 12:29:23: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:29:23: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:29:23: #1 total tags in treatment: 7767101 INFO @ Tue, 21 Apr 2015 12:29:23: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:29:23: #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 12:29:24: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:29:24: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:29:24: #1 total tags in treatment: 7767101 INFO @ Tue, 21 Apr 2015 12:29:24: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:29:24: #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 12:29:24: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:29:24: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:29:24: #1 total tags in treatment: 7767101 INFO @ Tue, 21 Apr 2015 12:29:24: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:29:24: #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 12:29:25: #1 tags after filtering in treatment: 7766169 INFO @ Tue, 21 Apr 2015 12:29:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:29:25: #1 finished! INFO @ Tue, 21 Apr 2015 12:29:25: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:29:25: #1 tags after filtering in treatment: 7766169 INFO @ Tue, 21 Apr 2015 12:29:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:29:25: #1 finished! INFO @ Tue, 21 Apr 2015 12:29:25: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:29:26: #1 tags after filtering in treatment: 7766169 INFO @ Tue, 21 Apr 2015 12:29:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:29:26: #1 finished! INFO @ Tue, 21 Apr 2015 12:29:26: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:29:27: #2 number of paired peaks: 1384 INFO @ Tue, 21 Apr 2015 12:29:27: start model_add_line... INFO @ Tue, 21 Apr 2015 12:29:27: #2 number of paired peaks: 1384 INFO @ Tue, 21 Apr 2015 12:29:27: start model_add_line... INFO @ Tue, 21 Apr 2015 12:29:27: #2 number of paired peaks: 1384 INFO @ Tue, 21 Apr 2015 12:29:27: start model_add_line... INFO @ Tue, 21 Apr 2015 12:29:34: start X-correlation... INFO @ Tue, 21 Apr 2015 12:29:34: end of X-cor INFO @ Tue, 21 Apr 2015 12:29:34: #2 finished! INFO @ Tue, 21 Apr 2015 12:29:34: #2 predicted fragment length is 103 bps INFO @ Tue, 21 Apr 2015 12:29:34: #2 alternative fragment length(s) may be 103 bps INFO @ Tue, 21 Apr 2015 12:29:34: #2.2 Generate R script for model : SRX018160.05_model.r INFO @ Tue, 21 Apr 2015 12:29:34: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:29:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:29:34: start X-correlation... INFO @ Tue, 21 Apr 2015 12:29:34: end of X-cor INFO @ Tue, 21 Apr 2015 12:29:34: #2 finished! INFO @ Tue, 21 Apr 2015 12:29:34: #2 predicted fragment length is 103 bps INFO @ Tue, 21 Apr 2015 12:29:34: #2 alternative fragment length(s) may be 103 bps INFO @ Tue, 21 Apr 2015 12:29:34: #2.2 Generate R script for model : SRX018160.10_model.r INFO @ Tue, 21 Apr 2015 12:29:34: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:29:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:29:35: start X-correlation... INFO @ Tue, 21 Apr 2015 12:29:35: end of X-cor INFO @ Tue, 21 Apr 2015 12:29:35: #2 finished! INFO @ Tue, 21 Apr 2015 12:29:35: #2 predicted fragment length is 103 bps INFO @ Tue, 21 Apr 2015 12:29:35: #2 alternative fragment length(s) may be 103 bps INFO @ Tue, 21 Apr 2015 12:29:35: #2.2 Generate R script for model : SRX018160.20_model.r INFO @ Tue, 21 Apr 2015 12:29:35: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:29:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:30:17: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:30:18: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:30:18: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:30:50: #4 Write output xls file... SRX018160.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:30:50: #4 Write peak in narrowPeak format file... SRX018160.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:30:50: #4 Write summits bed file... SRX018160.20_summits.bed INFO @ Tue, 21 Apr 2015 12:30:50: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1693 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:30:52: #4 Write output xls file... SRX018160.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:30:52: #4 Write peak in narrowPeak format file... SRX018160.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:30:52: #4 Write summits bed file... SRX018160.05_summits.bed INFO @ Tue, 21 Apr 2015 12:30:52: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5937 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:30:53: #4 Write output xls file... SRX018160.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:30:53: #4 Write peak in narrowPeak format file... SRX018160.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:30:53: #4 Write summits bed file... SRX018160.10_summits.bed INFO @ Tue, 21 Apr 2015 12:30:53: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3328 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。