Job ID = 2162052 sra ファイルのダウンロード中... Completed: 2600886K bytes transferred in 26 seconds (791606K 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 4007 0 4007 0 0 6722 0 --:--:-- --:--:-- --:--:-- 9893 100 35892 0 35892 0 0 45656 0 --:--:-- --:--:-- --:--:-- 60322 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 31108001 spots for /home/okishinya/chipatlas/results/dm3/SRX046656/SRR121524.sra Written 31108001 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: 00:59:06 31108001 reads; of these: 31108001 (100.00%) were paired; of these: 14314603 (46.02%) aligned concordantly 0 times 12425505 (39.94%) aligned concordantly exactly 1 time 4367893 (14.04%) aligned concordantly >1 times ---- 14314603 pairs aligned concordantly 0 times; of these: 1349275 (9.43%) aligned discordantly 1 time ---- 12965328 pairs aligned 0 times concordantly or discordantly; of these: 25930656 mates make up the pairs; of these: 22898054 (88.30%) aligned 0 times 1562095 (6.02%) aligned exactly 1 time 1470507 (5.67%) aligned >1 times 63.20% overall alignment rate Time searching: 00:59:06 Overall time: 00:59:06 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] 563125 / 18052503 = 0.0312 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 14:44:13: # Command line: callpeak -t SRX046656.bam -f BAM -g dm -n SRX046656.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX046656.10 # format = BAM # ChIP-seq file = ['SRX046656.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 14:44:13: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:44:13: # Command line: callpeak -t SRX046656.bam -f BAM -g dm -n SRX046656.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX046656.20 # format = BAM # ChIP-seq file = ['SRX046656.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 14:44:13: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:44:13: # Command line: callpeak -t SRX046656.bam -f BAM -g dm -n SRX046656.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX046656.05 # format = BAM # ChIP-seq file = ['SRX046656.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 14:44:13: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:44:13: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:44:13: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:44:13: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:44:20: 1000000 INFO @ Tue, 21 Apr 2015 14:44:20: 1000000 INFO @ Tue, 21 Apr 2015 14:44:20: 1000000 INFO @ Tue, 21 Apr 2015 14:44:27: 2000000 INFO @ Tue, 21 Apr 2015 14:44:28: 2000000 INFO @ Tue, 21 Apr 2015 14:44:28: 2000000 INFO @ Tue, 21 Apr 2015 14:44:33: 3000000 INFO @ Tue, 21 Apr 2015 14:44:35: 3000000 INFO @ Tue, 21 Apr 2015 14:44:35: 3000000 INFO @ Tue, 21 Apr 2015 14:44:40: 4000000 INFO @ Tue, 21 Apr 2015 14:44:42: 4000000 INFO @ Tue, 21 Apr 2015 14:44:42: 4000000 INFO @ Tue, 21 Apr 2015 14:44:46: 5000000 INFO @ Tue, 21 Apr 2015 14:44:49: 5000000 INFO @ Tue, 21 Apr 2015 14:44:49: 5000000 INFO @ Tue, 21 Apr 2015 14:44:53: 6000000 INFO @ Tue, 21 Apr 2015 14:44:56: 6000000 INFO @ Tue, 21 Apr 2015 14:44:56: 6000000 INFO @ Tue, 21 Apr 2015 14:44:59: 7000000 INFO @ Tue, 21 Apr 2015 14:45:03: 7000000 INFO @ Tue, 21 Apr 2015 14:45:03: 7000000 INFO @ Tue, 21 Apr 2015 14:45:06: 8000000 INFO @ Tue, 21 Apr 2015 14:45:10: 8000000 INFO @ Tue, 21 Apr 2015 14:45:10: 8000000 INFO @ Tue, 21 Apr 2015 14:45:12: 9000000 INFO @ Tue, 21 Apr 2015 14:45:17: 9000000 INFO @ Tue, 21 Apr 2015 14:45:18: 9000000 INFO @ Tue, 21 Apr 2015 14:45:18: 10000000 INFO @ Tue, 21 Apr 2015 14:45:25: 10000000 INFO @ Tue, 21 Apr 2015 14:45:25: 10000000 INFO @ Tue, 21 Apr 2015 14:45:25: 11000000 INFO @ Tue, 21 Apr 2015 14:45:31: 12000000 INFO @ Tue, 21 Apr 2015 14:45:32: 11000000 INFO @ Tue, 21 Apr 2015 14:45:32: 11000000 INFO @ Tue, 21 Apr 2015 14:45:38: 13000000 INFO @ Tue, 21 Apr 2015 14:45:39: 12000000 INFO @ Tue, 21 Apr 2015 14:45:39: 12000000 INFO @ Tue, 21 Apr 2015 14:45:44: 14000000 INFO @ Tue, 21 Apr 2015 14:45:46: 13000000 INFO @ Tue, 21 Apr 2015 14:45:46: 13000000 INFO @ Tue, 21 Apr 2015 14:45:51: 15000000 INFO @ Tue, 21 Apr 2015 14:45:53: 14000000 INFO @ Tue, 21 Apr 2015 14:45:53: 14000000 INFO @ Tue, 21 Apr 2015 14:45:57: 16000000 INFO @ Tue, 21 Apr 2015 14:46:00: 15000000 INFO @ Tue, 21 Apr 2015 14:46:00: 15000000 INFO @ Tue, 21 Apr 2015 14:46:04: 17000000 INFO @ Tue, 21 Apr 2015 14:46:08: 16000000 INFO @ Tue, 21 Apr 2015 14:46:08: 16000000 INFO @ Tue, 21 Apr 2015 14:46:10: 18000000 INFO @ Tue, 21 Apr 2015 14:46:15: 17000000 INFO @ Tue, 21 Apr 2015 14:46:15: 17000000 INFO @ Tue, 21 Apr 2015 14:46:17: 19000000 INFO @ Tue, 21 Apr 2015 14:46:22: 18000000 INFO @ Tue, 21 Apr 2015 14:46:22: 18000000 INFO @ Tue, 21 Apr 2015 14:46:23: 20000000 INFO @ Tue, 21 Apr 2015 14:46:29: 19000000 INFO @ Tue, 21 Apr 2015 14:46:29: 19000000 INFO @ Tue, 21 Apr 2015 14:46:30: 21000000 INFO @ Tue, 21 Apr 2015 14:46:36: 22000000 INFO @ Tue, 21 Apr 2015 14:46:36: 20000000 INFO @ Tue, 21 Apr 2015 14:46:36: 20000000 INFO @ Tue, 21 Apr 2015 14:46:43: 23000000 INFO @ Tue, 21 Apr 2015 14:46:43: 21000000 INFO @ Tue, 21 Apr 2015 14:46:43: 21000000 INFO @ Tue, 21 Apr 2015 14:46:49: 24000000 INFO @ Tue, 21 Apr 2015 14:46:51: 22000000 INFO @ Tue, 21 Apr 2015 14:46:51: 22000000 INFO @ Tue, 21 Apr 2015 14:46:56: 25000000 INFO @ Tue, 21 Apr 2015 14:46:58: 23000000 INFO @ Tue, 21 Apr 2015 14:46:58: 23000000 INFO @ Tue, 21 Apr 2015 14:47:02: 26000000 INFO @ Tue, 21 Apr 2015 14:47:05: 24000000 INFO @ Tue, 21 Apr 2015 14:47:05: 24000000 INFO @ Tue, 21 Apr 2015 14:47:09: 27000000 INFO @ Tue, 21 Apr 2015 14:47:12: 25000000 INFO @ Tue, 21 Apr 2015 14:47:12: 25000000 INFO @ Tue, 21 Apr 2015 14:47:15: 28000000 INFO @ Tue, 21 Apr 2015 14:47:19: 26000000 INFO @ Tue, 21 Apr 2015 14:47:19: 26000000 INFO @ Tue, 21 Apr 2015 14:47:21: 29000000 INFO @ Tue, 21 Apr 2015 14:47:26: 27000000 INFO @ Tue, 21 Apr 2015 14:47:26: 27000000 INFO @ Tue, 21 Apr 2015 14:47:28: 30000000 INFO @ Tue, 21 Apr 2015 14:47:33: 28000000 INFO @ Tue, 21 Apr 2015 14:47:33: 28000000 INFO @ Tue, 21 Apr 2015 14:47:34: 31000000 INFO @ Tue, 21 Apr 2015 14:47:40: 29000000 INFO @ Tue, 21 Apr 2015 14:47:40: 29000000 INFO @ Tue, 21 Apr 2015 14:47:41: 32000000 INFO @ Tue, 21 Apr 2015 14:47:47: 33000000 INFO @ Tue, 21 Apr 2015 14:47:48: 30000000 INFO @ Tue, 21 Apr 2015 14:47:48: 30000000 INFO @ Tue, 21 Apr 2015 14:47:54: 34000000 INFO @ Tue, 21 Apr 2015 14:47:55: 31000000 INFO @ Tue, 21 Apr 2015 14:47:55: 31000000 INFO @ Tue, 21 Apr 2015 14:48:00: 35000000 INFO @ Tue, 21 Apr 2015 14:48:02: 32000000 INFO @ Tue, 21 Apr 2015 14:48:02: 32000000 INFO @ Tue, 21 Apr 2015 14:48:07: 36000000 INFO @ Tue, 21 Apr 2015 14:48:09: 33000000 INFO @ Tue, 21 Apr 2015 14:48:09: 33000000 INFO @ Tue, 21 Apr 2015 14:48:13: 37000000 INFO @ Tue, 21 Apr 2015 14:48:16: 34000000 INFO @ Tue, 21 Apr 2015 14:48:16: 34000000 INFO @ Tue, 21 Apr 2015 14:48:20: 38000000 INFO @ Tue, 21 Apr 2015 14:48:21: #1 tag size is determined as 75 bps INFO @ Tue, 21 Apr 2015 14:48:21: #1 tag size = 75 INFO @ Tue, 21 Apr 2015 14:48:21: #1 total tags in treatment: 16272107 INFO @ Tue, 21 Apr 2015 14:48:21: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:48:21: #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 14:48:23: 35000000 INFO @ Tue, 21 Apr 2015 14:48:23: 35000000 INFO @ Tue, 21 Apr 2015 14:48:24: #1 tags after filtering in treatment: 13789036 INFO @ Tue, 21 Apr 2015 14:48:24: #1 Redundant rate of treatment: 0.15 INFO @ Tue, 21 Apr 2015 14:48:24: #1 finished! INFO @ Tue, 21 Apr 2015 14:48:24: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:48:27: #2 number of paired peaks: 2326 INFO @ Tue, 21 Apr 2015 14:48:27: start model_add_line... INFO @ Tue, 21 Apr 2015 14:48:30: 36000000 INFO @ Tue, 21 Apr 2015 14:48:30: 36000000 INFO @ Tue, 21 Apr 2015 14:48:37: 37000000 INFO @ Tue, 21 Apr 2015 14:48:37: 37000000 INFO @ Tue, 21 Apr 2015 14:48:44: 38000000 INFO @ Tue, 21 Apr 2015 14:48:44: 38000000 INFO @ Tue, 21 Apr 2015 14:48:46: #1 tag size is determined as 75 bps INFO @ Tue, 21 Apr 2015 14:48:46: #1 tag size = 75 INFO @ Tue, 21 Apr 2015 14:48:46: #1 total tags in treatment: 16272107 INFO @ Tue, 21 Apr 2015 14:48:46: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:48:46: #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 14:48:46: #1 tag size is determined as 75 bps INFO @ Tue, 21 Apr 2015 14:48:46: #1 tag size = 75 INFO @ Tue, 21 Apr 2015 14:48:46: #1 total tags in treatment: 16272107 INFO @ Tue, 21 Apr 2015 14:48:46: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:48:46: #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 14:48:49: #1 tags after filtering in treatment: 13789036 INFO @ Tue, 21 Apr 2015 14:48:49: #1 Redundant rate of treatment: 0.15 INFO @ Tue, 21 Apr 2015 14:48:49: #1 finished! INFO @ Tue, 21 Apr 2015 14:48:49: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:48:49: #1 tags after filtering in treatment: 13789036 INFO @ Tue, 21 Apr 2015 14:48:49: #1 Redundant rate of treatment: 0.15 INFO @ Tue, 21 Apr 2015 14:48:49: #1 finished! INFO @ Tue, 21 Apr 2015 14:48:49: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:48:50: start X-correlation... INFO @ Tue, 21 Apr 2015 14:48:50: end of X-cor INFO @ Tue, 21 Apr 2015 14:48:50: #2 finished! INFO @ Tue, 21 Apr 2015 14:48:50: #2 predicted fragment length is 234 bps INFO @ Tue, 21 Apr 2015 14:48:50: #2 alternative fragment length(s) may be 234 bps INFO @ Tue, 21 Apr 2015 14:48:50: #2.2 Generate R script for model : SRX046656.20_model.r INFO @ Tue, 21 Apr 2015 14:48:50: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:48:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:48:52: #2 number of paired peaks: 2326 INFO @ Tue, 21 Apr 2015 14:48:52: start model_add_line... INFO @ Tue, 21 Apr 2015 14:48:52: #2 number of paired peaks: 2326 INFO @ Tue, 21 Apr 2015 14:48:52: start model_add_line... INFO @ Tue, 21 Apr 2015 14:49:15: start X-correlation... INFO @ Tue, 21 Apr 2015 14:49:15: end of X-cor INFO @ Tue, 21 Apr 2015 14:49:15: #2 finished! INFO @ Tue, 21 Apr 2015 14:49:15: #2 predicted fragment length is 234 bps INFO @ Tue, 21 Apr 2015 14:49:15: #2 alternative fragment length(s) may be 234 bps INFO @ Tue, 21 Apr 2015 14:49:15: #2.2 Generate R script for model : SRX046656.05_model.r INFO @ Tue, 21 Apr 2015 14:49:15: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:49:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:49:15: start X-correlation... INFO @ Tue, 21 Apr 2015 14:49:15: end of X-cor INFO @ Tue, 21 Apr 2015 14:49:15: #2 finished! INFO @ Tue, 21 Apr 2015 14:49:15: #2 predicted fragment length is 234 bps INFO @ Tue, 21 Apr 2015 14:49:15: #2 alternative fragment length(s) may be 234 bps INFO @ Tue, 21 Apr 2015 14:49:15: #2.2 Generate R script for model : SRX046656.10_model.r INFO @ Tue, 21 Apr 2015 14:49:15: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:49:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:50:15: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:50:42: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:50:43: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:51:10: #4 Write output xls file... SRX046656.20_peaks.xls INFO @ Tue, 21 Apr 2015 14:51:10: #4 Write peak in narrowPeak format file... SRX046656.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:51:10: #4 Write summits bed file... SRX046656.20_summits.bed INFO @ Tue, 21 Apr 2015 14:51:10: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1793 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:51:40: #4 Write output xls file... SRX046656.10_peaks.xls INFO @ Tue, 21 Apr 2015 14:51:40: #4 Write peak in narrowPeak format file... SRX046656.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:51:40: #4 Write summits bed file... SRX046656.10_summits.bed INFO @ Tue, 21 Apr 2015 14:51:40: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4141 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:51:51: #4 Write output xls file... SRX046656.05_peaks.xls INFO @ Tue, 21 Apr 2015 14:51:51: #4 Write peak in narrowPeak format file... SRX046656.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:51:51: #4 Write summits bed file... SRX046656.05_summits.bed INFO @ Tue, 21 Apr 2015 14:51:51: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7431 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。