Job ID = 2162056 sra ファイルのダウンロード中... Completed: 2356004K bytes transferred in 17 seconds (1101983K 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 --:--:-- --:--:-- --:--:-- 0 101 5460 0 5460 0 0 9761 0 --:--:-- --:--:-- --:--:-- 14796 100 35882 0 35882 0 0 47904 0 --:--:-- --:--:-- --:--:-- 64304 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 28320021 spots for /home/okishinya/chipatlas/results/dm3/SRX046660/SRR121547.sra Written 28320021 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: 01:52:50 28320021 reads; of these: 28320021 (100.00%) were paired; of these: 7138642 (25.21%) aligned concordantly 0 times 14154657 (49.98%) aligned concordantly exactly 1 time 7026722 (24.81%) aligned concordantly >1 times ---- 7138642 pairs aligned concordantly 0 times; of these: 1210325 (16.95%) aligned discordantly 1 time ---- 5928317 pairs aligned 0 times concordantly or discordantly; of these: 11856634 mates make up the pairs; of these: 8930033 (75.32%) aligned 0 times 1398626 (11.80%) aligned exactly 1 time 1527975 (12.89%) aligned >1 times 84.23% overall alignment rate Time searching: 01:52:50 Overall time: 01:52:50 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] 811167 / 22274485 = 0.0364 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 15:44:36: # Command line: callpeak -t SRX046660.bam -f BAM -g dm -n SRX046660.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX046660.20 # format = BAM # ChIP-seq file = ['SRX046660.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 15:44:36: # Command line: callpeak -t SRX046660.bam -f BAM -g dm -n SRX046660.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX046660.05 # format = BAM # ChIP-seq file = ['SRX046660.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 15:44:36: # Command line: callpeak -t SRX046660.bam -f BAM -g dm -n SRX046660.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX046660.10 # format = BAM # ChIP-seq file = ['SRX046660.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 15:44:36: #1 read tag files... INFO @ Tue, 21 Apr 2015 15:44:36: #1 read tag files... INFO @ Tue, 21 Apr 2015 15:44:36: #1 read tag files... INFO @ Tue, 21 Apr 2015 15:44:36: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 15:44:36: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 15:44:36: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 15:44:42: 1000000 INFO @ Tue, 21 Apr 2015 15:44:43: 1000000 INFO @ Tue, 21 Apr 2015 15:44:43: 1000000 INFO @ Tue, 21 Apr 2015 15:44:49: 2000000 INFO @ Tue, 21 Apr 2015 15:44:50: 2000000 INFO @ Tue, 21 Apr 2015 15:44:50: 2000000 INFO @ Tue, 21 Apr 2015 15:44:55: 3000000 INFO @ Tue, 21 Apr 2015 15:44:57: 3000000 INFO @ Tue, 21 Apr 2015 15:44:58: 3000000 INFO @ Tue, 21 Apr 2015 15:45:02: 4000000 INFO @ Tue, 21 Apr 2015 15:45:05: 4000000 INFO @ Tue, 21 Apr 2015 15:45:05: 4000000 INFO @ Tue, 21 Apr 2015 15:45:08: 5000000 INFO @ Tue, 21 Apr 2015 15:45:12: 5000000 INFO @ Tue, 21 Apr 2015 15:45:12: 5000000 INFO @ Tue, 21 Apr 2015 15:45:15: 6000000 INFO @ Tue, 21 Apr 2015 15:45:18: 6000000 INFO @ Tue, 21 Apr 2015 15:45:19: 6000000 INFO @ Tue, 21 Apr 2015 15:45:22: 7000000 INFO @ Tue, 21 Apr 2015 15:45:25: 7000000 INFO @ Tue, 21 Apr 2015 15:45:26: 7000000 INFO @ Tue, 21 Apr 2015 15:45:29: 8000000 INFO @ Tue, 21 Apr 2015 15:45:31: 8000000 INFO @ Tue, 21 Apr 2015 15:45:33: 8000000 INFO @ Tue, 21 Apr 2015 15:45:37: 9000000 INFO @ Tue, 21 Apr 2015 15:45:38: 9000000 INFO @ Tue, 21 Apr 2015 15:45:40: 9000000 INFO @ Tue, 21 Apr 2015 15:45:44: 10000000 INFO @ Tue, 21 Apr 2015 15:45:44: 10000000 INFO @ Tue, 21 Apr 2015 15:45:47: 10000000 INFO @ Tue, 21 Apr 2015 15:45:51: 11000000 INFO @ Tue, 21 Apr 2015 15:45:51: 11000000 INFO @ Tue, 21 Apr 2015 15:45:54: 11000000 INFO @ Tue, 21 Apr 2015 15:45:58: 12000000 INFO @ Tue, 21 Apr 2015 15:45:58: 12000000 INFO @ Tue, 21 Apr 2015 15:46:01: 12000000 INFO @ Tue, 21 Apr 2015 15:46:04: 13000000 INFO @ Tue, 21 Apr 2015 15:46:05: 13000000 INFO @ Tue, 21 Apr 2015 15:46:09: 13000000 INFO @ Tue, 21 Apr 2015 15:46:11: 14000000 INFO @ Tue, 21 Apr 2015 15:46:12: 14000000 INFO @ Tue, 21 Apr 2015 15:46:16: 14000000 INFO @ Tue, 21 Apr 2015 15:46:17: 15000000 INFO @ Tue, 21 Apr 2015 15:46:20: 15000000 INFO @ Tue, 21 Apr 2015 15:46:23: 15000000 INFO @ Tue, 21 Apr 2015 15:46:24: 16000000 INFO @ Tue, 21 Apr 2015 15:46:27: 16000000 INFO @ Tue, 21 Apr 2015 15:46:30: 16000000 INFO @ Tue, 21 Apr 2015 15:46:31: 17000000 INFO @ Tue, 21 Apr 2015 15:46:34: 17000000 INFO @ Tue, 21 Apr 2015 15:46:37: 18000000 INFO @ Tue, 21 Apr 2015 15:46:37: 17000000 INFO @ Tue, 21 Apr 2015 15:46:41: 18000000 INFO @ Tue, 21 Apr 2015 15:46:44: 19000000 INFO @ Tue, 21 Apr 2015 15:46:45: 18000000 INFO @ Tue, 21 Apr 2015 15:46:48: 19000000 INFO @ Tue, 21 Apr 2015 15:46:50: 20000000 INFO @ Tue, 21 Apr 2015 15:46:52: 19000000 INFO @ Tue, 21 Apr 2015 15:46:56: 20000000 INFO @ Tue, 21 Apr 2015 15:46:57: 21000000 INFO @ Tue, 21 Apr 2015 15:46:59: 20000000 INFO @ Tue, 21 Apr 2015 15:47:03: 21000000 INFO @ Tue, 21 Apr 2015 15:47:04: 22000000 INFO @ Tue, 21 Apr 2015 15:47:06: 21000000 INFO @ Tue, 21 Apr 2015 15:47:10: 22000000 INFO @ Tue, 21 Apr 2015 15:47:10: 23000000 INFO @ Tue, 21 Apr 2015 15:47:13: 22000000 INFO @ Tue, 21 Apr 2015 15:47:17: 24000000 INFO @ Tue, 21 Apr 2015 15:47:17: 23000000 INFO @ Tue, 21 Apr 2015 15:47:21: 23000000 INFO @ Tue, 21 Apr 2015 15:47:23: 25000000 INFO @ Tue, 21 Apr 2015 15:47:24: 24000000 INFO @ Tue, 21 Apr 2015 15:47:28: 24000000 INFO @ Tue, 21 Apr 2015 15:47:30: 26000000 INFO @ Tue, 21 Apr 2015 15:47:32: 25000000 INFO @ Tue, 21 Apr 2015 15:47:35: 25000000 INFO @ Tue, 21 Apr 2015 15:47:37: 27000000 INFO @ Tue, 21 Apr 2015 15:47:39: 26000000 INFO @ Tue, 21 Apr 2015 15:47:43: 26000000 INFO @ Tue, 21 Apr 2015 15:47:44: 28000000 INFO @ Tue, 21 Apr 2015 15:47:46: 27000000 INFO @ Tue, 21 Apr 2015 15:47:50: 27000000 INFO @ Tue, 21 Apr 2015 15:47:50: 29000000 INFO @ Tue, 21 Apr 2015 15:47:54: 28000000 INFO @ Tue, 21 Apr 2015 15:47:57: 30000000 INFO @ Tue, 21 Apr 2015 15:47:57: 28000000 INFO @ Tue, 21 Apr 2015 15:48:01: 29000000 INFO @ Tue, 21 Apr 2015 15:48:04: 31000000 INFO @ Tue, 21 Apr 2015 15:48:04: 29000000 INFO @ Tue, 21 Apr 2015 15:48:08: 30000000 INFO @ Tue, 21 Apr 2015 15:48:11: 32000000 INFO @ Tue, 21 Apr 2015 15:48:12: 30000000 INFO @ Tue, 21 Apr 2015 15:48:16: 31000000 INFO @ Tue, 21 Apr 2015 15:48:17: 33000000 INFO @ Tue, 21 Apr 2015 15:48:19: 31000000 INFO @ Tue, 21 Apr 2015 15:48:23: 32000000 INFO @ Tue, 21 Apr 2015 15:48:24: 34000000 INFO @ Tue, 21 Apr 2015 15:48:26: 32000000 INFO @ Tue, 21 Apr 2015 15:48:30: 33000000 INFO @ Tue, 21 Apr 2015 15:48:31: 35000000 INFO @ Tue, 21 Apr 2015 15:48:34: 33000000 INFO @ Tue, 21 Apr 2015 15:48:38: 34000000 INFO @ Tue, 21 Apr 2015 15:48:38: 36000000 INFO @ Tue, 21 Apr 2015 15:48:41: 34000000 INFO @ Tue, 21 Apr 2015 15:48:45: 37000000 INFO @ Tue, 21 Apr 2015 15:48:45: 35000000 INFO @ Tue, 21 Apr 2015 15:48:49: 35000000 INFO @ Tue, 21 Apr 2015 15:48:52: 38000000 INFO @ Tue, 21 Apr 2015 15:48:53: 36000000 INFO @ Tue, 21 Apr 2015 15:48:56: 36000000 INFO @ Tue, 21 Apr 2015 15:48:59: 39000000 INFO @ Tue, 21 Apr 2015 15:49:00: 37000000 INFO @ Tue, 21 Apr 2015 15:49:03: 37000000 INFO @ Tue, 21 Apr 2015 15:49:06: 40000000 INFO @ Tue, 21 Apr 2015 15:49:07: 38000000 INFO @ Tue, 21 Apr 2015 15:49:11: 38000000 INFO @ Tue, 21 Apr 2015 15:49:13: 41000000 INFO @ Tue, 21 Apr 2015 15:49:15: 39000000 INFO @ Tue, 21 Apr 2015 15:49:18: 39000000 INFO @ Tue, 21 Apr 2015 15:49:20: 42000000 INFO @ Tue, 21 Apr 2015 15:49:22: 40000000 INFO @ Tue, 21 Apr 2015 15:49:26: 40000000 INFO @ Tue, 21 Apr 2015 15:49:27: 43000000 INFO @ Tue, 21 Apr 2015 15:49:30: 41000000 INFO @ Tue, 21 Apr 2015 15:49:33: 41000000 INFO @ Tue, 21 Apr 2015 15:49:33: 44000000 INFO @ Tue, 21 Apr 2015 15:49:37: 42000000 INFO @ Tue, 21 Apr 2015 15:49:40: 42000000 INFO @ Tue, 21 Apr 2015 15:49:40: 45000000 INFO @ Tue, 21 Apr 2015 15:49:44: 43000000 INFO @ Tue, 21 Apr 2015 15:49:47: 43000000 INFO @ Tue, 21 Apr 2015 15:49:47: 46000000 INFO @ Tue, 21 Apr 2015 15:49:48: #1 tag size is determined as 75 bps INFO @ Tue, 21 Apr 2015 15:49:48: #1 tag size = 75 INFO @ Tue, 21 Apr 2015 15:49:48: #1 total tags in treatment: 20414651 INFO @ Tue, 21 Apr 2015 15:49:48: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 15:49:48: #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 15:49:51: 44000000 INFO @ Tue, 21 Apr 2015 15:49:52: #1 tags after filtering in treatment: 17530833 INFO @ Tue, 21 Apr 2015 15:49:52: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 21 Apr 2015 15:49:52: #1 finished! INFO @ Tue, 21 Apr 2015 15:49:52: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 15:49:53: 44000000 INFO @ Tue, 21 Apr 2015 15:49:56: #2 number of paired peaks: 955 WARNING @ Tue, 21 Apr 2015 15:49:56: Fewer paired peaks (955) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 955 pairs to build model! INFO @ Tue, 21 Apr 2015 15:49:56: start model_add_line... INFO @ Tue, 21 Apr 2015 15:49:58: 45000000 INFO @ Tue, 21 Apr 2015 15:50:00: 45000000 INFO @ Tue, 21 Apr 2015 15:50:05: 46000000 INFO @ Tue, 21 Apr 2015 15:50:06: #1 tag size is determined as 75 bps INFO @ Tue, 21 Apr 2015 15:50:06: #1 tag size = 75 INFO @ Tue, 21 Apr 2015 15:50:06: #1 total tags in treatment: 20414651 INFO @ Tue, 21 Apr 2015 15:50:06: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 15:50:06: #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 15:50:07: 46000000 INFO @ Tue, 21 Apr 2015 15:50:07: start X-correlation... INFO @ Tue, 21 Apr 2015 15:50:07: end of X-cor INFO @ Tue, 21 Apr 2015 15:50:07: #2 finished! INFO @ Tue, 21 Apr 2015 15:50:07: #2 predicted fragment length is 188 bps INFO @ Tue, 21 Apr 2015 15:50:07: #2 alternative fragment length(s) may be 188 bps INFO @ Tue, 21 Apr 2015 15:50:07: #2.2 Generate R script for model : SRX046660.20_model.r INFO @ Tue, 21 Apr 2015 15:50:07: #3 Call peaks... INFO @ Tue, 21 Apr 2015 15:50:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 15:50:07: #1 tag size is determined as 75 bps INFO @ Tue, 21 Apr 2015 15:50:07: #1 tag size = 75 INFO @ Tue, 21 Apr 2015 15:50:07: #1 total tags in treatment: 20414651 INFO @ Tue, 21 Apr 2015 15:50:07: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 15:50:07: #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 15:50:10: #1 tags after filtering in treatment: 17530833 INFO @ Tue, 21 Apr 2015 15:50:10: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 21 Apr 2015 15:50:10: #1 finished! INFO @ Tue, 21 Apr 2015 15:50:10: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 15:50:11: #1 tags after filtering in treatment: 17530833 INFO @ Tue, 21 Apr 2015 15:50:11: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 21 Apr 2015 15:50:11: #1 finished! INFO @ Tue, 21 Apr 2015 15:50:11: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 15:50:13: #2 number of paired peaks: 955 WARNING @ Tue, 21 Apr 2015 15:50:13: Fewer paired peaks (955) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 955 pairs to build model! INFO @ Tue, 21 Apr 2015 15:50:13: start model_add_line... INFO @ Tue, 21 Apr 2015 15:50:14: #2 number of paired peaks: 955 WARNING @ Tue, 21 Apr 2015 15:50:14: Fewer paired peaks (955) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 955 pairs to build model! INFO @ Tue, 21 Apr 2015 15:50:14: start model_add_line... INFO @ Tue, 21 Apr 2015 15:50:24: start X-correlation... INFO @ Tue, 21 Apr 2015 15:50:24: end of X-cor INFO @ Tue, 21 Apr 2015 15:50:24: #2 finished! INFO @ Tue, 21 Apr 2015 15:50:24: #2 predicted fragment length is 188 bps INFO @ Tue, 21 Apr 2015 15:50:24: #2 alternative fragment length(s) may be 188 bps INFO @ Tue, 21 Apr 2015 15:50:24: #2.2 Generate R script for model : SRX046660.05_model.r INFO @ Tue, 21 Apr 2015 15:50:24: #3 Call peaks... INFO @ Tue, 21 Apr 2015 15:50:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 15:50:26: start X-correlation... INFO @ Tue, 21 Apr 2015 15:50:26: end of X-cor INFO @ Tue, 21 Apr 2015 15:50:26: #2 finished! INFO @ Tue, 21 Apr 2015 15:50:26: #2 predicted fragment length is 188 bps INFO @ Tue, 21 Apr 2015 15:50:26: #2 alternative fragment length(s) may be 188 bps INFO @ Tue, 21 Apr 2015 15:50:26: #2.2 Generate R script for model : SRX046660.10_model.r INFO @ Tue, 21 Apr 2015 15:50:26: #3 Call peaks... INFO @ Tue, 21 Apr 2015 15:50:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 15:51:41: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 15:51:58: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 15:52:08: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 15:52:47: #4 Write output xls file... SRX046660.20_peaks.xls INFO @ Tue, 21 Apr 2015 15:52:47: #4 Write peak in narrowPeak format file... SRX046660.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 15:52:47: #4 Write summits bed file... SRX046660.20_summits.bed INFO @ Tue, 21 Apr 2015 15:52:47: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1932 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 15:53:16: #4 Write output xls file... SRX046660.05_peaks.xls INFO @ Tue, 21 Apr 2015 15:53:16: #4 Write peak in narrowPeak format file... SRX046660.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 15:53:16: #4 Write summits bed file... SRX046660.05_summits.bed INFO @ Tue, 21 Apr 2015 15:53:16: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8047 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 15:53:22: #4 Write output xls file... SRX046660.10_peaks.xls INFO @ Tue, 21 Apr 2015 15:53:22: #4 Write peak in narrowPeak format file... SRX046660.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 15:53:22: #4 Write summits bed file... SRX046660.10_summits.bed INFO @ Tue, 21 Apr 2015 15:53:22: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3867 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。