Job ID = 2162053 sra ファイルのダウンロード中... Completed: 2440199K bytes transferred in 30 seconds (660261K 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 36108 0 36108 0 0 46533 0 --:--:-- --:--:-- --:--:-- 61828 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 27798910 spots for /home/okishinya/chipatlas/results/dm3/SRX046657/SRR121532.sra Written 27798910 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: 00:37:21 27798910 reads; of these: 27798910 (100.00%) were paired; of these: 6714112 (24.15%) aligned concordantly 0 times 19134719 (68.83%) aligned concordantly exactly 1 time 1950079 (7.01%) aligned concordantly >1 times ---- 6714112 pairs aligned concordantly 0 times; of these: 1944385 (28.96%) aligned discordantly 1 time ---- 4769727 pairs aligned 0 times concordantly or discordantly; of these: 9539454 mates make up the pairs; of these: 7493504 (78.55%) aligned 0 times 1503170 (15.76%) aligned exactly 1 time 542780 (5.69%) aligned >1 times 86.52% overall alignment rate Time searching: 00:37:21 Overall time: 00:37:21 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] 1310114 / 22960320 = 0.0571 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 14:25:54: # Command line: callpeak -t SRX046657.bam -f BAM -g dm -n SRX046657.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX046657.10 # format = BAM # ChIP-seq file = ['SRX046657.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 14:25:54: # Command line: callpeak -t SRX046657.bam -f BAM -g dm -n SRX046657.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX046657.05 # format = BAM # ChIP-seq file = ['SRX046657.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 14:25:54: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:25:54: # Command line: callpeak -t SRX046657.bam -f BAM -g dm -n SRX046657.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX046657.20 # format = BAM # ChIP-seq file = ['SRX046657.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 14:25:54: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:25:54: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:25:54: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:25:54: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:25:54: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:26:01: 1000000 INFO @ Tue, 21 Apr 2015 14:26:01: 1000000 INFO @ Tue, 21 Apr 2015 14:26:01: 1000000 INFO @ Tue, 21 Apr 2015 14:26:07: 2000000 INFO @ Tue, 21 Apr 2015 14:26:09: 2000000 INFO @ Tue, 21 Apr 2015 14:26:09: 2000000 INFO @ Tue, 21 Apr 2015 14:26:14: 3000000 INFO @ Tue, 21 Apr 2015 14:26:16: 3000000 INFO @ Tue, 21 Apr 2015 14:26:16: 3000000 INFO @ Tue, 21 Apr 2015 14:26:21: 4000000 INFO @ Tue, 21 Apr 2015 14:26:23: 4000000 INFO @ Tue, 21 Apr 2015 14:26:23: 4000000 INFO @ Tue, 21 Apr 2015 14:26:27: 5000000 INFO @ Tue, 21 Apr 2015 14:26:30: 5000000 INFO @ Tue, 21 Apr 2015 14:26:30: 5000000 INFO @ Tue, 21 Apr 2015 14:26:33: 6000000 INFO @ Tue, 21 Apr 2015 14:26:36: 6000000 INFO @ Tue, 21 Apr 2015 14:26:36: 6000000 INFO @ Tue, 21 Apr 2015 14:26:40: 7000000 INFO @ Tue, 21 Apr 2015 14:26:43: 7000000 INFO @ Tue, 21 Apr 2015 14:26:43: 7000000 INFO @ Tue, 21 Apr 2015 14:26:46: 8000000 INFO @ Tue, 21 Apr 2015 14:26:50: 8000000 INFO @ Tue, 21 Apr 2015 14:26:50: 8000000 INFO @ Tue, 21 Apr 2015 14:26:52: 9000000 INFO @ Tue, 21 Apr 2015 14:26:57: 9000000 INFO @ Tue, 21 Apr 2015 14:26:57: 9000000 INFO @ Tue, 21 Apr 2015 14:26:59: 10000000 INFO @ Tue, 21 Apr 2015 14:27:04: 10000000 INFO @ Tue, 21 Apr 2015 14:27:04: 10000000 INFO @ Tue, 21 Apr 2015 14:27:05: 11000000 INFO @ Tue, 21 Apr 2015 14:27:11: 11000000 INFO @ Tue, 21 Apr 2015 14:27:11: 12000000 INFO @ Tue, 21 Apr 2015 14:27:11: 11000000 INFO @ Tue, 21 Apr 2015 14:27:18: 13000000 INFO @ Tue, 21 Apr 2015 14:27:18: 12000000 INFO @ Tue, 21 Apr 2015 14:27:18: 12000000 INFO @ Tue, 21 Apr 2015 14:27:24: 14000000 INFO @ Tue, 21 Apr 2015 14:27:25: 13000000 INFO @ Tue, 21 Apr 2015 14:27:25: 13000000 INFO @ Tue, 21 Apr 2015 14:27:30: 15000000 INFO @ Tue, 21 Apr 2015 14:27:32: 14000000 INFO @ Tue, 21 Apr 2015 14:27:32: 14000000 INFO @ Tue, 21 Apr 2015 14:27:37: 16000000 INFO @ Tue, 21 Apr 2015 14:27:39: 15000000 INFO @ Tue, 21 Apr 2015 14:27:39: 15000000 INFO @ Tue, 21 Apr 2015 14:27:43: 17000000 INFO @ Tue, 21 Apr 2015 14:27:46: 16000000 INFO @ Tue, 21 Apr 2015 14:27:46: 16000000 INFO @ Tue, 21 Apr 2015 14:27:49: 18000000 INFO @ Tue, 21 Apr 2015 14:27:53: 17000000 INFO @ Tue, 21 Apr 2015 14:27:53: 17000000 INFO @ Tue, 21 Apr 2015 14:27:56: 19000000 INFO @ Tue, 21 Apr 2015 14:28:01: 18000000 INFO @ Tue, 21 Apr 2015 14:28:01: 18000000 INFO @ Tue, 21 Apr 2015 14:28:03: 20000000 INFO @ Tue, 21 Apr 2015 14:28:09: 19000000 INFO @ Tue, 21 Apr 2015 14:28:10: 19000000 INFO @ Tue, 21 Apr 2015 14:28:11: 21000000 INFO @ Tue, 21 Apr 2015 14:28:18: 20000000 INFO @ Tue, 21 Apr 2015 14:28:18: 20000000 INFO @ Tue, 21 Apr 2015 14:28:19: 22000000 INFO @ Tue, 21 Apr 2015 14:28:26: 21000000 INFO @ Tue, 21 Apr 2015 14:28:26: 23000000 INFO @ Tue, 21 Apr 2015 14:28:26: 21000000 INFO @ Tue, 21 Apr 2015 14:28:32: 24000000 INFO @ Tue, 21 Apr 2015 14:28:33: 22000000 INFO @ Tue, 21 Apr 2015 14:28:33: 22000000 INFO @ Tue, 21 Apr 2015 14:28:39: 25000000 INFO @ Tue, 21 Apr 2015 14:28:40: 23000000 INFO @ Tue, 21 Apr 2015 14:28:40: 23000000 INFO @ Tue, 21 Apr 2015 14:28:45: 26000000 INFO @ Tue, 21 Apr 2015 14:28:47: 24000000 INFO @ Tue, 21 Apr 2015 14:28:48: 24000000 INFO @ Tue, 21 Apr 2015 14:28:51: 27000000 INFO @ Tue, 21 Apr 2015 14:28:54: 25000000 INFO @ Tue, 21 Apr 2015 14:28:55: 25000000 INFO @ Tue, 21 Apr 2015 14:28:58: 28000000 INFO @ Tue, 21 Apr 2015 14:29:01: 26000000 INFO @ Tue, 21 Apr 2015 14:29:02: 26000000 INFO @ Tue, 21 Apr 2015 14:29:04: 29000000 INFO @ Tue, 21 Apr 2015 14:29:08: 27000000 INFO @ Tue, 21 Apr 2015 14:29:09: 27000000 INFO @ Tue, 21 Apr 2015 14:29:10: 30000000 INFO @ Tue, 21 Apr 2015 14:29:16: 28000000 INFO @ Tue, 21 Apr 2015 14:29:17: 28000000 INFO @ Tue, 21 Apr 2015 14:29:17: 31000000 INFO @ Tue, 21 Apr 2015 14:29:23: 29000000 INFO @ Tue, 21 Apr 2015 14:29:23: 32000000 INFO @ Tue, 21 Apr 2015 14:29:24: 29000000 INFO @ Tue, 21 Apr 2015 14:29:29: 33000000 INFO @ Tue, 21 Apr 2015 14:29:30: 30000000 INFO @ Tue, 21 Apr 2015 14:29:31: 30000000 INFO @ Tue, 21 Apr 2015 14:29:36: 34000000 INFO @ Tue, 21 Apr 2015 14:29:37: 31000000 INFO @ Tue, 21 Apr 2015 14:29:38: 31000000 INFO @ Tue, 21 Apr 2015 14:29:42: 35000000 INFO @ Tue, 21 Apr 2015 14:29:44: 32000000 INFO @ Tue, 21 Apr 2015 14:29:45: 32000000 INFO @ Tue, 21 Apr 2015 14:29:49: 36000000 INFO @ Tue, 21 Apr 2015 14:29:51: 33000000 INFO @ Tue, 21 Apr 2015 14:29:52: 33000000 INFO @ Tue, 21 Apr 2015 14:29:55: 37000000 INFO @ Tue, 21 Apr 2015 14:29:58: 34000000 INFO @ Tue, 21 Apr 2015 14:29:59: 34000000 INFO @ Tue, 21 Apr 2015 14:30:02: 38000000 INFO @ Tue, 21 Apr 2015 14:30:05: 35000000 INFO @ Tue, 21 Apr 2015 14:30:05: 35000000 INFO @ Tue, 21 Apr 2015 14:30:09: 39000000 INFO @ Tue, 21 Apr 2015 14:30:12: 36000000 INFO @ Tue, 21 Apr 2015 14:30:12: 36000000 INFO @ Tue, 21 Apr 2015 14:30:17: 40000000 INFO @ Tue, 21 Apr 2015 14:30:18: 37000000 INFO @ Tue, 21 Apr 2015 14:30:19: 37000000 INFO @ Tue, 21 Apr 2015 14:30:24: 41000000 INFO @ Tue, 21 Apr 2015 14:30:25: 38000000 INFO @ Tue, 21 Apr 2015 14:30:26: 38000000 INFO @ Tue, 21 Apr 2015 14:30:31: 42000000 INFO @ Tue, 21 Apr 2015 14:30:31: 39000000 INFO @ Tue, 21 Apr 2015 14:30:33: 39000000 INFO @ Tue, 21 Apr 2015 14:30:38: 40000000 INFO @ Tue, 21 Apr 2015 14:30:38: 43000000 INFO @ Tue, 21 Apr 2015 14:30:40: 40000000 INFO @ Tue, 21 Apr 2015 14:30:44: 41000000 INFO @ Tue, 21 Apr 2015 14:30:45: 44000000 INFO @ Tue, 21 Apr 2015 14:30:46: 41000000 INFO @ Tue, 21 Apr 2015 14:30:50: 42000000 INFO @ Tue, 21 Apr 2015 14:30:52: 45000000 INFO @ Tue, 21 Apr 2015 14:30:53: 42000000 INFO @ Tue, 21 Apr 2015 14:30:56: #1 tag size is determined as 75 bps INFO @ Tue, 21 Apr 2015 14:30:56: #1 tag size = 75 INFO @ Tue, 21 Apr 2015 14:30:56: #1 total tags in treatment: 19847488 INFO @ Tue, 21 Apr 2015 14:30:56: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:30:56: #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 14:30:57: 43000000 INFO @ Tue, 21 Apr 2015 14:30:59: #1 tags after filtering in treatment: 13150338 INFO @ Tue, 21 Apr 2015 14:30:59: #1 Redundant rate of treatment: 0.34 INFO @ Tue, 21 Apr 2015 14:30:59: #1 finished! INFO @ Tue, 21 Apr 2015 14:30:59: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:31:00: 43000000 INFO @ Tue, 21 Apr 2015 14:31:03: #2 number of paired peaks: 12494 INFO @ Tue, 21 Apr 2015 14:31:03: start model_add_line... INFO @ Tue, 21 Apr 2015 14:31:04: 44000000 INFO @ Tue, 21 Apr 2015 14:31:06: 44000000 INFO @ Tue, 21 Apr 2015 14:31:10: 45000000 INFO @ Tue, 21 Apr 2015 14:31:13: 45000000 INFO @ Tue, 21 Apr 2015 14:31:13: #1 tag size is determined as 75 bps INFO @ Tue, 21 Apr 2015 14:31:13: #1 tag size = 75 INFO @ Tue, 21 Apr 2015 14:31:13: #1 total tags in treatment: 19847488 INFO @ Tue, 21 Apr 2015 14:31:13: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:31:13: #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 14:31:16: #1 tag size is determined as 75 bps INFO @ Tue, 21 Apr 2015 14:31:16: #1 tag size = 75 INFO @ Tue, 21 Apr 2015 14:31:16: #1 total tags in treatment: 19847488 INFO @ Tue, 21 Apr 2015 14:31:16: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:31:16: #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 14:31:17: #1 tags after filtering in treatment: 13150338 INFO @ Tue, 21 Apr 2015 14:31:17: #1 Redundant rate of treatment: 0.34 INFO @ Tue, 21 Apr 2015 14:31:17: #1 finished! INFO @ Tue, 21 Apr 2015 14:31:17: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:31:20: #1 tags after filtering in treatment: 13150338 INFO @ Tue, 21 Apr 2015 14:31:20: #1 Redundant rate of treatment: 0.34 INFO @ Tue, 21 Apr 2015 14:31:20: #1 finished! INFO @ Tue, 21 Apr 2015 14:31:20: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:31:21: #2 number of paired peaks: 12494 INFO @ Tue, 21 Apr 2015 14:31:21: start model_add_line... INFO @ Tue, 21 Apr 2015 14:31:24: #2 number of paired peaks: 12494 INFO @ Tue, 21 Apr 2015 14:31:24: start model_add_line... INFO @ Tue, 21 Apr 2015 14:33:02: start X-correlation... INFO @ Tue, 21 Apr 2015 14:33:02: end of X-cor INFO @ Tue, 21 Apr 2015 14:33:02: #2 finished! INFO @ Tue, 21 Apr 2015 14:33:02: #2 predicted fragment length is 249 bps INFO @ Tue, 21 Apr 2015 14:33:02: #2 alternative fragment length(s) may be 249 bps INFO @ Tue, 21 Apr 2015 14:33:02: #2.2 Generate R script for model : SRX046657.10_model.r INFO @ Tue, 21 Apr 2015 14:33:02: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:33:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:33:19: start X-correlation... INFO @ Tue, 21 Apr 2015 14:33:19: end of X-cor INFO @ Tue, 21 Apr 2015 14:33:19: #2 finished! INFO @ Tue, 21 Apr 2015 14:33:19: #2 predicted fragment length is 249 bps INFO @ Tue, 21 Apr 2015 14:33:19: #2 alternative fragment length(s) may be 249 bps INFO @ Tue, 21 Apr 2015 14:33:19: #2.2 Generate R script for model : SRX046657.05_model.r INFO @ Tue, 21 Apr 2015 14:33:19: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:33:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:33:22: start X-correlation... INFO @ Tue, 21 Apr 2015 14:33:22: end of X-cor INFO @ Tue, 21 Apr 2015 14:33:22: #2 finished! INFO @ Tue, 21 Apr 2015 14:33:22: #2 predicted fragment length is 249 bps INFO @ Tue, 21 Apr 2015 14:33:22: #2 alternative fragment length(s) may be 249 bps INFO @ Tue, 21 Apr 2015 14:33:22: #2.2 Generate R script for model : SRX046657.20_model.r INFO @ Tue, 21 Apr 2015 14:33:22: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:33:22: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 21 Apr 2015 14:34:51: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 21 Apr 2015 14:35:10: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:35:11: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:36:02: #4 Write output xls file... SRX046657.10_peaks.xls INFO @ Tue, 21 Apr 2015 14:36:02: #4 Write peak in narrowPeak format file... SRX046657.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:36:02: #4 Write summits bed file... SRX046657.10_summits.bed INFO @ Tue, 21 Apr 2015 14:36:03: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (10259 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:36:16: #4 Write output xls file... SRX046657.20_peaks.xls INFO @ Tue, 21 Apr 2015 14:36:16: #4 Write peak in narrowPeak format file... SRX046657.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:36:16: #4 Write summits bed file... SRX046657.20_summits.bed INFO @ Tue, 21 Apr 2015 14:36:17: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7779 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:36:27: #4 Write output xls file... SRX046657.05_peaks.xls INFO @ Tue, 21 Apr 2015 14:36:28: #4 Write peak in narrowPeak format file... SRX046657.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:36:28: #4 Write summits bed file... SRX046657.05_summits.bed INFO @ Tue, 21 Apr 2015 14:36:28: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (12335 records, 4 fields): 16 millis CompletedMACS2peakCalling