Job ID = 2162055 sra ファイルのダウンロード中... Completed: 2414311K bytes transferred in 29 seconds (676284K 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 35885 0 35885 0 0 47655 0 --:--:-- --:--:-- --:--:-- 63966 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 29489149 spots for /home/okishinya/chipatlas/results/dm3/SRX046659/SRR121546.sra Written 29489149 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: 02:01:03 29489149 reads; of these: 29489149 (100.00%) were paired; of these: 4780957 (16.21%) aligned concordantly 0 times 16563986 (56.17%) aligned concordantly exactly 1 time 8144206 (27.62%) aligned concordantly >1 times ---- 4780957 pairs aligned concordantly 0 times; of these: 1385084 (28.97%) aligned discordantly 1 time ---- 3395873 pairs aligned 0 times concordantly or discordantly; of these: 6791746 mates make up the pairs; of these: 4348057 (64.02%) aligned 0 times 988407 (14.55%) aligned exactly 1 time 1455282 (21.43%) aligned >1 times 92.63% overall alignment rate Time searching: 02:01:03 Overall time: 02:01:03 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 24 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] 1095587 / 26025354 = 0.0421 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 15:54:30: # Command line: callpeak -t SRX046659.bam -f BAM -g dm -n SRX046659.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX046659.20 # format = BAM # ChIP-seq file = ['SRX046659.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 15:54:30: # Command line: callpeak -t SRX046659.bam -f BAM -g dm -n SRX046659.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX046659.05 # format = BAM # ChIP-seq file = ['SRX046659.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 15:54:30: #1 read tag files... INFO @ Tue, 21 Apr 2015 15:54:30: #1 read tag files... INFO @ Tue, 21 Apr 2015 15:54:30: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 15:54:30: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 15:54:30: # Command line: callpeak -t SRX046659.bam -f BAM -g dm -n SRX046659.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX046659.10 # format = BAM # ChIP-seq file = ['SRX046659.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 15:54:30: #1 read tag files... INFO @ Tue, 21 Apr 2015 15:54:30: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 15:54:37: 1000000 INFO @ Tue, 21 Apr 2015 15:54:37: 1000000 INFO @ Tue, 21 Apr 2015 15:54:37: 1000000 INFO @ Tue, 21 Apr 2015 15:54:44: 2000000 INFO @ Tue, 21 Apr 2015 15:54:44: 2000000 INFO @ Tue, 21 Apr 2015 15:54:44: 2000000 INFO @ Tue, 21 Apr 2015 15:54:50: 3000000 INFO @ Tue, 21 Apr 2015 15:54:52: 3000000 INFO @ Tue, 21 Apr 2015 15:54:52: 3000000 INFO @ Tue, 21 Apr 2015 15:54:56: 4000000 INFO @ Tue, 21 Apr 2015 15:54:59: 4000000 INFO @ Tue, 21 Apr 2015 15:54:59: 4000000 INFO @ Tue, 21 Apr 2015 15:55:03: 5000000 INFO @ Tue, 21 Apr 2015 15:55:06: 5000000 INFO @ Tue, 21 Apr 2015 15:55:06: 5000000 INFO @ Tue, 21 Apr 2015 15:55:09: 6000000 INFO @ Tue, 21 Apr 2015 15:55:13: 6000000 INFO @ Tue, 21 Apr 2015 15:55:13: 6000000 INFO @ Tue, 21 Apr 2015 15:55:16: 7000000 INFO @ Tue, 21 Apr 2015 15:55:20: 7000000 INFO @ Tue, 21 Apr 2015 15:55:20: 7000000 INFO @ Tue, 21 Apr 2015 15:55:22: 8000000 INFO @ Tue, 21 Apr 2015 15:55:27: 8000000 INFO @ Tue, 21 Apr 2015 15:55:27: 8000000 INFO @ Tue, 21 Apr 2015 15:55:29: 9000000 INFO @ Tue, 21 Apr 2015 15:55:34: 9000000 INFO @ Tue, 21 Apr 2015 15:55:34: 9000000 INFO @ Tue, 21 Apr 2015 15:55:35: 10000000 INFO @ Tue, 21 Apr 2015 15:55:41: 10000000 INFO @ Tue, 21 Apr 2015 15:55:41: 10000000 INFO @ Tue, 21 Apr 2015 15:55:42: 11000000 INFO @ Tue, 21 Apr 2015 15:55:48: 11000000 INFO @ Tue, 21 Apr 2015 15:55:48: 11000000 INFO @ Tue, 21 Apr 2015 15:55:48: 12000000 INFO @ Tue, 21 Apr 2015 15:55:55: 13000000 INFO @ Tue, 21 Apr 2015 15:55:55: 12000000 INFO @ Tue, 21 Apr 2015 15:55:55: 12000000 INFO @ Tue, 21 Apr 2015 15:56:01: 14000000 INFO @ Tue, 21 Apr 2015 15:56:02: 13000000 INFO @ Tue, 21 Apr 2015 15:56:02: 13000000 INFO @ Tue, 21 Apr 2015 15:56:08: 15000000 INFO @ Tue, 21 Apr 2015 15:56:09: 14000000 INFO @ Tue, 21 Apr 2015 15:56:09: 14000000 INFO @ Tue, 21 Apr 2015 15:56:14: 16000000 INFO @ Tue, 21 Apr 2015 15:56:16: 15000000 INFO @ Tue, 21 Apr 2015 15:56:16: 15000000 INFO @ Tue, 21 Apr 2015 15:56:21: 17000000 INFO @ Tue, 21 Apr 2015 15:56:23: 16000000 INFO @ Tue, 21 Apr 2015 15:56:23: 16000000 INFO @ Tue, 21 Apr 2015 15:56:27: 18000000 INFO @ Tue, 21 Apr 2015 15:56:30: 17000000 INFO @ Tue, 21 Apr 2015 15:56:30: 17000000 INFO @ Tue, 21 Apr 2015 15:56:34: 19000000 INFO @ Tue, 21 Apr 2015 15:56:38: 18000000 INFO @ Tue, 21 Apr 2015 15:56:38: 18000000 INFO @ Tue, 21 Apr 2015 15:56:40: 20000000 INFO @ Tue, 21 Apr 2015 15:56:45: 19000000 INFO @ Tue, 21 Apr 2015 15:56:45: 19000000 INFO @ Tue, 21 Apr 2015 15:56:47: 21000000 INFO @ Tue, 21 Apr 2015 15:56:52: 20000000 INFO @ Tue, 21 Apr 2015 15:56:52: 20000000 INFO @ Tue, 21 Apr 2015 15:56:53: 22000000 INFO @ Tue, 21 Apr 2015 15:56:59: 21000000 INFO @ Tue, 21 Apr 2015 15:56:59: 21000000 INFO @ Tue, 21 Apr 2015 15:57:00: 23000000 INFO @ Tue, 21 Apr 2015 15:57:06: 22000000 INFO @ Tue, 21 Apr 2015 15:57:06: 22000000 INFO @ Tue, 21 Apr 2015 15:57:06: 24000000 INFO @ Tue, 21 Apr 2015 15:57:13: 23000000 INFO @ Tue, 21 Apr 2015 15:57:13: 23000000 INFO @ Tue, 21 Apr 2015 15:57:13: 25000000 INFO @ Tue, 21 Apr 2015 15:57:19: 26000000 INFO @ Tue, 21 Apr 2015 15:57:20: 24000000 INFO @ Tue, 21 Apr 2015 15:57:20: 24000000 INFO @ Tue, 21 Apr 2015 15:57:26: 27000000 INFO @ Tue, 21 Apr 2015 15:57:27: 25000000 INFO @ Tue, 21 Apr 2015 15:57:27: 25000000 INFO @ Tue, 21 Apr 2015 15:57:32: 28000000 INFO @ Tue, 21 Apr 2015 15:57:34: 26000000 INFO @ Tue, 21 Apr 2015 15:57:34: 26000000 INFO @ Tue, 21 Apr 2015 15:57:39: 29000000 INFO @ Tue, 21 Apr 2015 15:57:41: 27000000 INFO @ Tue, 21 Apr 2015 15:57:41: 27000000 INFO @ Tue, 21 Apr 2015 15:57:45: 30000000 INFO @ Tue, 21 Apr 2015 15:57:48: 28000000 INFO @ Tue, 21 Apr 2015 15:57:48: 28000000 INFO @ Tue, 21 Apr 2015 15:57:52: 31000000 INFO @ Tue, 21 Apr 2015 15:57:55: 29000000 INFO @ Tue, 21 Apr 2015 15:57:55: 29000000 INFO @ Tue, 21 Apr 2015 15:57:58: 32000000 INFO @ Tue, 21 Apr 2015 15:58:02: 30000000 INFO @ Tue, 21 Apr 2015 15:58:02: 30000000 INFO @ Tue, 21 Apr 2015 15:58:05: 33000000 INFO @ Tue, 21 Apr 2015 15:58:09: 31000000 INFO @ Tue, 21 Apr 2015 15:58:09: 31000000 INFO @ Tue, 21 Apr 2015 15:58:11: 34000000 INFO @ Tue, 21 Apr 2015 15:58:17: 32000000 INFO @ Tue, 21 Apr 2015 15:58:17: 32000000 INFO @ Tue, 21 Apr 2015 15:58:18: 35000000 INFO @ Tue, 21 Apr 2015 15:58:24: 33000000 INFO @ Tue, 21 Apr 2015 15:58:24: 33000000 INFO @ Tue, 21 Apr 2015 15:58:25: 36000000 INFO @ Tue, 21 Apr 2015 15:58:31: 34000000 INFO @ Tue, 21 Apr 2015 15:58:31: 34000000 INFO @ Tue, 21 Apr 2015 15:58:31: 37000000 INFO @ Tue, 21 Apr 2015 15:58:38: 35000000 INFO @ Tue, 21 Apr 2015 15:58:38: 35000000 INFO @ Tue, 21 Apr 2015 15:58:38: 38000000 INFO @ Tue, 21 Apr 2015 15:58:45: 36000000 INFO @ Tue, 21 Apr 2015 15:58:45: 36000000 INFO @ Tue, 21 Apr 2015 15:58:45: 39000000 INFO @ Tue, 21 Apr 2015 15:58:51: 40000000 INFO @ Tue, 21 Apr 2015 15:58:52: 37000000 INFO @ Tue, 21 Apr 2015 15:58:52: 37000000 INFO @ Tue, 21 Apr 2015 15:58:58: 41000000 INFO @ Tue, 21 Apr 2015 15:58:59: 38000000 INFO @ Tue, 21 Apr 2015 15:58:59: 38000000 INFO @ Tue, 21 Apr 2015 15:59:05: 42000000 INFO @ Tue, 21 Apr 2015 15:59:06: 39000000 INFO @ Tue, 21 Apr 2015 15:59:06: 39000000 INFO @ Tue, 21 Apr 2015 15:59:11: 43000000 INFO @ Tue, 21 Apr 2015 15:59:13: 40000000 INFO @ Tue, 21 Apr 2015 15:59:13: 40000000 INFO @ Tue, 21 Apr 2015 15:59:18: 44000000 INFO @ Tue, 21 Apr 2015 15:59:20: 41000000 INFO @ Tue, 21 Apr 2015 15:59:20: 41000000 INFO @ Tue, 21 Apr 2015 15:59:25: 45000000 INFO @ Tue, 21 Apr 2015 15:59:27: 42000000 INFO @ Tue, 21 Apr 2015 15:59:27: 42000000 INFO @ Tue, 21 Apr 2015 15:59:31: 46000000 INFO @ Tue, 21 Apr 2015 15:59:34: 43000000 INFO @ Tue, 21 Apr 2015 15:59:34: 43000000 INFO @ Tue, 21 Apr 2015 15:59:38: 47000000 INFO @ Tue, 21 Apr 2015 15:59:41: 44000000 INFO @ Tue, 21 Apr 2015 15:59:41: 44000000 INFO @ Tue, 21 Apr 2015 15:59:45: 48000000 INFO @ Tue, 21 Apr 2015 15:59:49: 45000000 INFO @ Tue, 21 Apr 2015 15:59:49: 45000000 INFO @ Tue, 21 Apr 2015 15:59:51: 49000000 INFO @ Tue, 21 Apr 2015 15:59:56: 46000000 INFO @ Tue, 21 Apr 2015 15:59:56: 46000000 INFO @ Tue, 21 Apr 2015 15:59:58: 50000000 INFO @ Tue, 21 Apr 2015 16:00:03: 47000000 INFO @ Tue, 21 Apr 2015 16:00:03: 47000000 INFO @ Tue, 21 Apr 2015 16:00:05: 51000000 INFO @ Tue, 21 Apr 2015 16:00:10: 48000000 INFO @ Tue, 21 Apr 2015 16:00:10: 48000000 INFO @ Tue, 21 Apr 2015 16:00:11: 52000000 INFO @ Tue, 21 Apr 2015 16:00:14: #1 tag size is determined as 75 bps INFO @ Tue, 21 Apr 2015 16:00:14: #1 tag size = 75 INFO @ Tue, 21 Apr 2015 16:00:14: #1 total tags in treatment: 23696179 INFO @ Tue, 21 Apr 2015 16:00:14: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 16:00:14: #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 16:00:17: 49000000 INFO @ Tue, 21 Apr 2015 16:00:17: 49000000 INFO @ Tue, 21 Apr 2015 16:00:19: #1 tags after filtering in treatment: 20127410 INFO @ Tue, 21 Apr 2015 16:00:19: #1 Redundant rate of treatment: 0.15 INFO @ Tue, 21 Apr 2015 16:00:19: #1 finished! INFO @ Tue, 21 Apr 2015 16:00:19: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 16:00:22: #2 number of paired peaks: 827 WARNING @ Tue, 21 Apr 2015 16:00:22: Fewer paired peaks (827) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 827 pairs to build model! INFO @ Tue, 21 Apr 2015 16:00:22: start model_add_line... INFO @ Tue, 21 Apr 2015 16:00:24: 50000000 INFO @ Tue, 21 Apr 2015 16:00:24: 50000000 INFO @ Tue, 21 Apr 2015 16:00:31: 51000000 INFO @ Tue, 21 Apr 2015 16:00:32: 51000000 INFO @ Tue, 21 Apr 2015 16:00:34: start X-correlation... INFO @ Tue, 21 Apr 2015 16:00:34: end of X-cor INFO @ Tue, 21 Apr 2015 16:00:34: #2 finished! INFO @ Tue, 21 Apr 2015 16:00:34: #2 predicted fragment length is 198 bps INFO @ Tue, 21 Apr 2015 16:00:34: #2 alternative fragment length(s) may be 198 bps INFO @ Tue, 21 Apr 2015 16:00:34: #2.2 Generate R script for model : SRX046659.10_model.r INFO @ Tue, 21 Apr 2015 16:00:34: #3 Call peaks... INFO @ Tue, 21 Apr 2015 16:00:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 16:00:39: 52000000 INFO @ Tue, 21 Apr 2015 16:00:39: 52000000 INFO @ Tue, 21 Apr 2015 16:00:42: #1 tag size is determined as 75 bps INFO @ Tue, 21 Apr 2015 16:00:42: #1 tag size = 75 INFO @ Tue, 21 Apr 2015 16:00:42: #1 total tags in treatment: 23696179 INFO @ Tue, 21 Apr 2015 16:00:42: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 16:00:42: #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 16:00:42: #1 tag size is determined as 75 bps INFO @ Tue, 21 Apr 2015 16:00:42: #1 tag size = 75 INFO @ Tue, 21 Apr 2015 16:00:42: #1 total tags in treatment: 23696179 INFO @ Tue, 21 Apr 2015 16:00:42: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 16:00:42: #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 16:00:46: #1 tags after filtering in treatment: 20127410 INFO @ Tue, 21 Apr 2015 16:00:46: #1 Redundant rate of treatment: 0.15 INFO @ Tue, 21 Apr 2015 16:00:46: #1 finished! INFO @ Tue, 21 Apr 2015 16:00:46: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 16:00:46: #1 tags after filtering in treatment: 20127410 INFO @ Tue, 21 Apr 2015 16:00:46: #1 Redundant rate of treatment: 0.15 INFO @ Tue, 21 Apr 2015 16:00:46: #1 finished! INFO @ Tue, 21 Apr 2015 16:00:46: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 16:00:50: #2 number of paired peaks: 827 WARNING @ Tue, 21 Apr 2015 16:00:50: Fewer paired peaks (827) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 827 pairs to build model! INFO @ Tue, 21 Apr 2015 16:00:50: start model_add_line... INFO @ Tue, 21 Apr 2015 16:00:50: #2 number of paired peaks: 827 WARNING @ Tue, 21 Apr 2015 16:00:50: Fewer paired peaks (827) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 827 pairs to build model! INFO @ Tue, 21 Apr 2015 16:00:50: start model_add_line... INFO @ Tue, 21 Apr 2015 16:01:00: start X-correlation... INFO @ Tue, 21 Apr 2015 16:01:00: end of X-cor INFO @ Tue, 21 Apr 2015 16:01:00: #2 finished! INFO @ Tue, 21 Apr 2015 16:01:00: #2 predicted fragment length is 198 bps INFO @ Tue, 21 Apr 2015 16:01:00: #2 alternative fragment length(s) may be 198 bps INFO @ Tue, 21 Apr 2015 16:01:00: #2.2 Generate R script for model : SRX046659.20_model.r INFO @ Tue, 21 Apr 2015 16:01:00: #3 Call peaks... INFO @ Tue, 21 Apr 2015 16:01:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 16:01:01: start X-correlation... INFO @ Tue, 21 Apr 2015 16:01:01: end of X-cor INFO @ Tue, 21 Apr 2015 16:01:01: #2 finished! INFO @ Tue, 21 Apr 2015 16:01:01: #2 predicted fragment length is 198 bps INFO @ Tue, 21 Apr 2015 16:01:01: #2 alternative fragment length(s) may be 198 bps INFO @ Tue, 21 Apr 2015 16:01:01: #2.2 Generate R script for model : SRX046659.05_model.r INFO @ Tue, 21 Apr 2015 16:01:01: #3 Call peaks... INFO @ Tue, 21 Apr 2015 16:01:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 16:02:22: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 16:02:48: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 16:02:51: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 16:03:41: #4 Write output xls file... SRX046659.10_peaks.xls INFO @ Tue, 21 Apr 2015 16:03:41: #4 Write peak in narrowPeak format file... SRX046659.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 16:03:41: #4 Write summits bed file... SRX046659.10_summits.bed INFO @ Tue, 21 Apr 2015 16:03:41: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4539 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 16:04:06: #4 Write output xls file... SRX046659.20_peaks.xls INFO @ Tue, 21 Apr 2015 16:04:06: #4 Write peak in narrowPeak format file... SRX046659.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 16:04:06: #4 Write summits bed file... SRX046659.20_summits.bed INFO @ Tue, 21 Apr 2015 16:04:06: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (2156 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 16:04:18: #4 Write output xls file... SRX046659.05_peaks.xls INFO @ Tue, 21 Apr 2015 16:04:18: #4 Write peak in narrowPeak format file... SRX046659.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 16:04:18: #4 Write summits bed file... SRX046659.05_summits.bed INFO @ Tue, 21 Apr 2015 16:04:18: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9639 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。