Job ID = 2162054 sra ファイルのダウンロード中... Completed: 2271337K bytes transferred in 30 seconds (615545K 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 26566 0 26566 0 0 35117 0 --:--:-- --:--:-- --:--:-- 46936 100 35887 0 35887 0 0 47382 0 --:--:-- --:--:-- --:--:-- 63292 sra ファイルのダウンロードが完了しました。 Read layout: PAIRED fastq に変換中... Written 27730274 spots for /home/okishinya/chipatlas/results/dm3/SRX046658/SRR121540.sra Written 27730274 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: 00:48:59 27730274 reads; of these: 27730274 (100.00%) were paired; of these: 9520424 (34.33%) aligned concordantly 0 times 14459498 (52.14%) aligned concordantly exactly 1 time 3750352 (13.52%) aligned concordantly >1 times ---- 9520424 pairs aligned concordantly 0 times; of these: 968044 (10.17%) aligned discordantly 1 time ---- 8552380 pairs aligned 0 times concordantly or discordantly; of these: 17104760 mates make up the pairs; of these: 14254134 (83.33%) aligned 0 times 1685344 (9.85%) aligned exactly 1 time 1165282 (6.81%) aligned >1 times 74.30% overall alignment rate Time searching: 00:48:59 Overall time: 00:48:59 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 20 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 2565805 / 19012017 = 0.1350 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 14:34:16: # Command line: callpeak -t SRX046658.bam -f BAM -g dm -n SRX046658.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX046658.20 # format = BAM # ChIP-seq file = ['SRX046658.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 14:34:16: # Command line: callpeak -t SRX046658.bam -f BAM -g dm -n SRX046658.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX046658.10 # format = BAM # ChIP-seq file = ['SRX046658.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 14:34:16: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:34:16: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:34:16: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:34:16: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:34:16: # Command line: callpeak -t SRX046658.bam -f BAM -g dm -n SRX046658.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX046658.05 # format = BAM # ChIP-seq file = ['SRX046658.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 14:34:16: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:34:16: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:34:22: 1000000 INFO @ Tue, 21 Apr 2015 14:34:22: 1000000 INFO @ Tue, 21 Apr 2015 14:34:22: 1000000 INFO @ Tue, 21 Apr 2015 14:34:28: 2000000 INFO @ Tue, 21 Apr 2015 14:34:28: 2000000 INFO @ Tue, 21 Apr 2015 14:34:28: 2000000 INFO @ Tue, 21 Apr 2015 14:34:34: 3000000 INFO @ Tue, 21 Apr 2015 14:34:34: 3000000 INFO @ Tue, 21 Apr 2015 14:34:34: 3000000 INFO @ Tue, 21 Apr 2015 14:34:40: 4000000 INFO @ Tue, 21 Apr 2015 14:34:40: 4000000 INFO @ Tue, 21 Apr 2015 14:34:41: 4000000 INFO @ Tue, 21 Apr 2015 14:34:46: 5000000 INFO @ Tue, 21 Apr 2015 14:34:46: 5000000 INFO @ Tue, 21 Apr 2015 14:34:47: 5000000 INFO @ Tue, 21 Apr 2015 14:34:51: 6000000 INFO @ Tue, 21 Apr 2015 14:34:52: 6000000 INFO @ Tue, 21 Apr 2015 14:34:53: 6000000 INFO @ Tue, 21 Apr 2015 14:34:57: 7000000 INFO @ Tue, 21 Apr 2015 14:34:58: 7000000 INFO @ Tue, 21 Apr 2015 14:34:59: 7000000 INFO @ Tue, 21 Apr 2015 14:35:03: 8000000 INFO @ Tue, 21 Apr 2015 14:35:05: 8000000 INFO @ Tue, 21 Apr 2015 14:35:05: 8000000 INFO @ Tue, 21 Apr 2015 14:35:09: 9000000 INFO @ Tue, 21 Apr 2015 14:35:11: 9000000 INFO @ Tue, 21 Apr 2015 14:35:11: 9000000 INFO @ Tue, 21 Apr 2015 14:35:15: 10000000 INFO @ Tue, 21 Apr 2015 14:35:17: 10000000 INFO @ Tue, 21 Apr 2015 14:35:18: 10000000 INFO @ Tue, 21 Apr 2015 14:35:20: 11000000 INFO @ Tue, 21 Apr 2015 14:35:23: 11000000 INFO @ Tue, 21 Apr 2015 14:35:24: 11000000 INFO @ Tue, 21 Apr 2015 14:35:26: 12000000 INFO @ Tue, 21 Apr 2015 14:35:29: 12000000 INFO @ Tue, 21 Apr 2015 14:35:30: 12000000 INFO @ Tue, 21 Apr 2015 14:35:32: 13000000 INFO @ Tue, 21 Apr 2015 14:35:36: 13000000 INFO @ Tue, 21 Apr 2015 14:35:37: 13000000 INFO @ Tue, 21 Apr 2015 14:35:38: 14000000 INFO @ Tue, 21 Apr 2015 14:35:42: 14000000 INFO @ Tue, 21 Apr 2015 14:35:43: 14000000 INFO @ Tue, 21 Apr 2015 14:35:44: 15000000 INFO @ Tue, 21 Apr 2015 14:35:48: 15000000 INFO @ Tue, 21 Apr 2015 14:35:49: 16000000 INFO @ Tue, 21 Apr 2015 14:35:50: 15000000 INFO @ Tue, 21 Apr 2015 14:35:54: 16000000 INFO @ Tue, 21 Apr 2015 14:35:55: 17000000 INFO @ Tue, 21 Apr 2015 14:35:56: 16000000 INFO @ Tue, 21 Apr 2015 14:36:00: 17000000 INFO @ Tue, 21 Apr 2015 14:36:01: 18000000 INFO @ Tue, 21 Apr 2015 14:36:02: 17000000 INFO @ Tue, 21 Apr 2015 14:36:07: 18000000 INFO @ Tue, 21 Apr 2015 14:36:07: 19000000 INFO @ Tue, 21 Apr 2015 14:36:08: 18000000 INFO @ Tue, 21 Apr 2015 14:36:13: 20000000 INFO @ Tue, 21 Apr 2015 14:36:13: 19000000 INFO @ Tue, 21 Apr 2015 14:36:15: 19000000 INFO @ Tue, 21 Apr 2015 14:36:18: 21000000 INFO @ Tue, 21 Apr 2015 14:36:19: 20000000 INFO @ Tue, 21 Apr 2015 14:36:21: 20000000 INFO @ Tue, 21 Apr 2015 14:36:24: 22000000 INFO @ Tue, 21 Apr 2015 14:36:25: 21000000 INFO @ Tue, 21 Apr 2015 14:36:27: 21000000 INFO @ Tue, 21 Apr 2015 14:36:30: 23000000 INFO @ Tue, 21 Apr 2015 14:36:31: 22000000 INFO @ Tue, 21 Apr 2015 14:36:34: 22000000 INFO @ Tue, 21 Apr 2015 14:36:36: 24000000 INFO @ Tue, 21 Apr 2015 14:36:38: 23000000 INFO @ Tue, 21 Apr 2015 14:36:40: 23000000 INFO @ Tue, 21 Apr 2015 14:36:42: 25000000 INFO @ Tue, 21 Apr 2015 14:36:44: 24000000 INFO @ Tue, 21 Apr 2015 14:36:46: 24000000 INFO @ Tue, 21 Apr 2015 14:36:47: 26000000 INFO @ Tue, 21 Apr 2015 14:36:50: 25000000 INFO @ Tue, 21 Apr 2015 14:36:53: 25000000 INFO @ Tue, 21 Apr 2015 14:36:53: 27000000 INFO @ Tue, 21 Apr 2015 14:36:56: 26000000 INFO @ Tue, 21 Apr 2015 14:36:59: 28000000 INFO @ Tue, 21 Apr 2015 14:36:59: 26000000 INFO @ Tue, 21 Apr 2015 14:37:03: 27000000 INFO @ Tue, 21 Apr 2015 14:37:05: 29000000 INFO @ Tue, 21 Apr 2015 14:37:06: 27000000 INFO @ Tue, 21 Apr 2015 14:37:10: 28000000 INFO @ Tue, 21 Apr 2015 14:37:11: 30000000 INFO @ Tue, 21 Apr 2015 14:37:13: 28000000 INFO @ Tue, 21 Apr 2015 14:37:16: 29000000 INFO @ Tue, 21 Apr 2015 14:37:16: 31000000 INFO @ Tue, 21 Apr 2015 14:37:19: 29000000 INFO @ Tue, 21 Apr 2015 14:37:22: 32000000 INFO @ Tue, 21 Apr 2015 14:37:22: 30000000 INFO @ Tue, 21 Apr 2015 14:37:26: 30000000 INFO @ Tue, 21 Apr 2015 14:37:28: 33000000 INFO @ Tue, 21 Apr 2015 14:37:29: 31000000 INFO @ Tue, 21 Apr 2015 14:37:33: 31000000 INFO @ Tue, 21 Apr 2015 14:37:34: 34000000 INFO @ Tue, 21 Apr 2015 14:37:36: 32000000 INFO @ Tue, 21 Apr 2015 14:37:39: 32000000 INFO @ Tue, 21 Apr 2015 14:37:40: 35000000 INFO @ Tue, 21 Apr 2015 14:37:42: 33000000 INFO @ Tue, 21 Apr 2015 14:37:46: 36000000 INFO @ Tue, 21 Apr 2015 14:37:46: 33000000 INFO @ Tue, 21 Apr 2015 14:37:46: #1 tag size is determined as 75 bps INFO @ Tue, 21 Apr 2015 14:37:46: #1 tag size = 75 INFO @ Tue, 21 Apr 2015 14:37:46: #1 total tags in treatment: 15689847 INFO @ Tue, 21 Apr 2015 14:37:46: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:37:46: #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 14:37:49: 34000000 INFO @ Tue, 21 Apr 2015 14:37:49: #1 tags after filtering in treatment: 11548304 INFO @ Tue, 21 Apr 2015 14:37:49: #1 Redundant rate of treatment: 0.26 INFO @ Tue, 21 Apr 2015 14:37:49: #1 finished! INFO @ Tue, 21 Apr 2015 14:37:49: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:37:52: #2 number of paired peaks: 5997 INFO @ Tue, 21 Apr 2015 14:37:52: start model_add_line... INFO @ Tue, 21 Apr 2015 14:37:53: 34000000 INFO @ Tue, 21 Apr 2015 14:37:55: 35000000 INFO @ Tue, 21 Apr 2015 14:37:59: 35000000 INFO @ Tue, 21 Apr 2015 14:38:02: 36000000 INFO @ Tue, 21 Apr 2015 14:38:03: #1 tag size is determined as 75 bps INFO @ Tue, 21 Apr 2015 14:38:03: #1 tag size = 75 INFO @ Tue, 21 Apr 2015 14:38:03: #1 total tags in treatment: 15689847 INFO @ Tue, 21 Apr 2015 14:38:03: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:38:03: #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 14:38:06: #1 tags after filtering in treatment: 11548304 INFO @ Tue, 21 Apr 2015 14:38:06: #1 Redundant rate of treatment: 0.26 INFO @ Tue, 21 Apr 2015 14:38:06: #1 finished! INFO @ Tue, 21 Apr 2015 14:38:06: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:38:06: 36000000 INFO @ Tue, 21 Apr 2015 14:38:06: #1 tag size is determined as 75 bps INFO @ Tue, 21 Apr 2015 14:38:06: #1 tag size = 75 INFO @ Tue, 21 Apr 2015 14:38:06: #1 total tags in treatment: 15689847 INFO @ Tue, 21 Apr 2015 14:38:06: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:38:06: #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 14:38:08: #2 number of paired peaks: 5997 INFO @ Tue, 21 Apr 2015 14:38:08: start model_add_line... INFO @ Tue, 21 Apr 2015 14:38:09: #1 tags after filtering in treatment: 11548304 INFO @ Tue, 21 Apr 2015 14:38:09: #1 Redundant rate of treatment: 0.26 INFO @ Tue, 21 Apr 2015 14:38:09: #1 finished! INFO @ Tue, 21 Apr 2015 14:38:09: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:38:12: #2 number of paired peaks: 5997 INFO @ Tue, 21 Apr 2015 14:38:12: start model_add_line... INFO @ Tue, 21 Apr 2015 14:38:38: start X-correlation... INFO @ Tue, 21 Apr 2015 14:38:38: end of X-cor INFO @ Tue, 21 Apr 2015 14:38:38: #2 finished! INFO @ Tue, 21 Apr 2015 14:38:38: #2 predicted fragment length is 238 bps INFO @ Tue, 21 Apr 2015 14:38:38: #2 alternative fragment length(s) may be 238 bps INFO @ Tue, 21 Apr 2015 14:38:38: #2.2 Generate R script for model : SRX046658.05_model.r INFO @ Tue, 21 Apr 2015 14:38:38: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:38:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:38:52: start X-correlation... INFO @ Tue, 21 Apr 2015 14:38:52: end of X-cor INFO @ Tue, 21 Apr 2015 14:38:52: #2 finished! INFO @ Tue, 21 Apr 2015 14:38:52: #2 predicted fragment length is 238 bps INFO @ Tue, 21 Apr 2015 14:38:52: #2 alternative fragment length(s) may be 238 bps INFO @ Tue, 21 Apr 2015 14:38:52: #2.2 Generate R script for model : SRX046658.20_model.r INFO @ Tue, 21 Apr 2015 14:38:52: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:38:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:38:58: start X-correlation... INFO @ Tue, 21 Apr 2015 14:38:58: end of X-cor INFO @ Tue, 21 Apr 2015 14:38:58: #2 finished! INFO @ Tue, 21 Apr 2015 14:38:58: #2 predicted fragment length is 238 bps INFO @ Tue, 21 Apr 2015 14:38:58: #2 alternative fragment length(s) may be 238 bps INFO @ Tue, 21 Apr 2015 14:38:58: #2.2 Generate R script for model : SRX046658.10_model.r INFO @ Tue, 21 Apr 2015 14:38:58: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:38:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:40:00: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:40:14: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:40:19: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:41:09: #4 Write output xls file... SRX046658.05_peaks.xls INFO @ Tue, 21 Apr 2015 14:41:09: #4 Write peak in narrowPeak format file... SRX046658.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:41:09: #4 Write summits bed file... SRX046658.05_summits.bed INFO @ Tue, 21 Apr 2015 14:41:10: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (12351 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:41:11: #4 Write output xls file... SRX046658.20_peaks.xls INFO @ Tue, 21 Apr 2015 14:41:11: #4 Write peak in narrowPeak format file... SRX046658.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:41:11: #4 Write summits bed file... SRX046658.20_summits.bed INFO @ Tue, 21 Apr 2015 14:41:11: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6515 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:41:25: #4 Write output xls file... SRX046658.10_peaks.xls INFO @ Tue, 21 Apr 2015 14:41:25: #4 Write peak in narrowPeak format file... SRX046658.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:41:25: #4 Write summits bed file... SRX046658.10_summits.bed INFO @ Tue, 21 Apr 2015 14:41:25: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (9550 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。