Job ID = 9159861 sra ファイルのダウンロード中... Completed: 1291352K bytes transferred in 13 seconds (772321K bits/sec), in 1 file, 2 directories. 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 19721984 spots for /home/okishinya/chipatlas/results/dm3/SRX749065/SRR1636793.sra Written 19721984 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: 00:37:01 19721984 reads; of these: 19721984 (100.00%) were paired; of these: 1761005 (8.93%) aligned concordantly 0 times 14995122 (76.03%) aligned concordantly exactly 1 time 2965857 (15.04%) aligned concordantly >1 times ---- 1761005 pairs aligned concordantly 0 times; of these: 421679 (23.95%) aligned discordantly 1 time ---- 1339326 pairs aligned 0 times concordantly or discordantly; of these: 2678652 mates make up the pairs; of these: 1636111 (61.08%) aligned 0 times 688526 (25.70%) aligned exactly 1 time 354015 (13.22%) aligned >1 times 95.85% overall alignment rate Time searching: 00:37:01 Overall time: 00:37:01 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 16 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] 1511471 / 18363134 = 0.0823 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 @ Wed, 28 Jun 2017 01:11:37: # Command line: callpeak -t SRX749065.bam -f BAM -g dm -n SRX749065.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX749065.05 # format = BAM # ChIP-seq file = ['SRX749065.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 # Paired-End mode is off INFO @ Wed, 28 Jun 2017 01:11:37: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:11:37: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:11:37: # Command line: callpeak -t SRX749065.bam -f BAM -g dm -n SRX749065.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX749065.10 # format = BAM # ChIP-seq file = ['SRX749065.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 # Paired-End mode is off INFO @ Wed, 28 Jun 2017 01:11:37: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:11:37: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:11:37: # Command line: callpeak -t SRX749065.bam -f BAM -g dm -n SRX749065.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX749065.20 # format = BAM # ChIP-seq file = ['SRX749065.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 # Paired-End mode is off INFO @ Wed, 28 Jun 2017 01:11:37: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:11:37: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:11:43: 1000000 INFO @ Wed, 28 Jun 2017 01:11:43: 1000000 INFO @ Wed, 28 Jun 2017 01:11:43: 1000000 INFO @ Wed, 28 Jun 2017 01:11:48: 2000000 INFO @ Wed, 28 Jun 2017 01:11:48: 2000000 INFO @ Wed, 28 Jun 2017 01:11:48: 2000000 INFO @ Wed, 28 Jun 2017 01:11:54: 3000000 INFO @ Wed, 28 Jun 2017 01:11:54: 3000000 INFO @ Wed, 28 Jun 2017 01:11:54: 3000000 INFO @ Wed, 28 Jun 2017 01:12:00: 4000000 INFO @ Wed, 28 Jun 2017 01:12:00: 4000000 INFO @ Wed, 28 Jun 2017 01:12:00: 4000000 INFO @ Wed, 28 Jun 2017 01:12:06: 5000000 INFO @ Wed, 28 Jun 2017 01:12:06: 5000000 INFO @ Wed, 28 Jun 2017 01:12:06: 5000000 INFO @ Wed, 28 Jun 2017 01:12:12: 6000000 INFO @ Wed, 28 Jun 2017 01:12:12: 6000000 INFO @ Wed, 28 Jun 2017 01:12:12: 6000000 INFO @ Wed, 28 Jun 2017 01:12:17: 7000000 INFO @ Wed, 28 Jun 2017 01:12:18: 7000000 INFO @ Wed, 28 Jun 2017 01:12:18: 7000000 INFO @ Wed, 28 Jun 2017 01:12:23: 8000000 INFO @ Wed, 28 Jun 2017 01:12:23: 8000000 INFO @ Wed, 28 Jun 2017 01:12:23: 8000000 INFO @ Wed, 28 Jun 2017 01:12:29: 9000000 INFO @ Wed, 28 Jun 2017 01:12:29: 9000000 INFO @ Wed, 28 Jun 2017 01:12:29: 9000000 INFO @ Wed, 28 Jun 2017 01:12:34: 10000000 INFO @ Wed, 28 Jun 2017 01:12:35: 10000000 INFO @ Wed, 28 Jun 2017 01:12:35: 10000000 INFO @ Wed, 28 Jun 2017 01:12:40: 11000000 INFO @ Wed, 28 Jun 2017 01:12:40: 11000000 INFO @ Wed, 28 Jun 2017 01:12:40: 11000000 INFO @ Wed, 28 Jun 2017 01:12:46: 12000000 INFO @ Wed, 28 Jun 2017 01:12:46: 12000000 INFO @ Wed, 28 Jun 2017 01:12:46: 12000000 INFO @ Wed, 28 Jun 2017 01:12:51: 13000000 INFO @ Wed, 28 Jun 2017 01:12:52: 13000000 INFO @ Wed, 28 Jun 2017 01:12:52: 13000000 INFO @ Wed, 28 Jun 2017 01:12:57: 14000000 INFO @ Wed, 28 Jun 2017 01:12:58: 14000000 INFO @ Wed, 28 Jun 2017 01:12:58: 14000000 INFO @ Wed, 28 Jun 2017 01:13:03: 15000000 INFO @ Wed, 28 Jun 2017 01:13:03: 15000000 INFO @ Wed, 28 Jun 2017 01:13:03: 15000000 INFO @ Wed, 28 Jun 2017 01:13:08: 16000000 INFO @ Wed, 28 Jun 2017 01:13:09: 16000000 INFO @ Wed, 28 Jun 2017 01:13:09: 16000000 INFO @ Wed, 28 Jun 2017 01:13:14: 17000000 INFO @ Wed, 28 Jun 2017 01:13:15: 17000000 INFO @ Wed, 28 Jun 2017 01:13:15: 17000000 INFO @ Wed, 28 Jun 2017 01:13:20: 18000000 INFO @ Wed, 28 Jun 2017 01:13:21: 18000000 INFO @ Wed, 28 Jun 2017 01:13:21: 18000000 INFO @ Wed, 28 Jun 2017 01:13:25: 19000000 INFO @ Wed, 28 Jun 2017 01:13:26: 19000000 INFO @ Wed, 28 Jun 2017 01:13:27: 19000000 INFO @ Wed, 28 Jun 2017 01:13:31: 20000000 INFO @ Wed, 28 Jun 2017 01:13:32: 20000000 INFO @ Wed, 28 Jun 2017 01:13:32: 20000000 INFO @ Wed, 28 Jun 2017 01:13:37: 21000000 INFO @ Wed, 28 Jun 2017 01:13:38: 21000000 INFO @ Wed, 28 Jun 2017 01:13:38: 21000000 INFO @ Wed, 28 Jun 2017 01:13:42: 22000000 INFO @ Wed, 28 Jun 2017 01:13:44: 22000000 INFO @ Wed, 28 Jun 2017 01:13:44: 22000000 INFO @ Wed, 28 Jun 2017 01:13:48: 23000000 INFO @ Wed, 28 Jun 2017 01:13:50: 23000000 INFO @ Wed, 28 Jun 2017 01:13:50: 23000000 INFO @ Wed, 28 Jun 2017 01:13:54: 24000000 INFO @ Wed, 28 Jun 2017 01:13:55: 24000000 INFO @ Wed, 28 Jun 2017 01:13:56: 24000000 INFO @ Wed, 28 Jun 2017 01:13:59: 25000000 INFO @ Wed, 28 Jun 2017 01:14:01: 25000000 INFO @ Wed, 28 Jun 2017 01:14:02: 25000000 INFO @ Wed, 28 Jun 2017 01:14:05: 26000000 INFO @ Wed, 28 Jun 2017 01:14:07: 26000000 INFO @ Wed, 28 Jun 2017 01:14:08: 26000000 INFO @ Wed, 28 Jun 2017 01:14:11: 27000000 INFO @ Wed, 28 Jun 2017 01:14:13: 27000000 INFO @ Wed, 28 Jun 2017 01:14:14: 27000000 INFO @ Wed, 28 Jun 2017 01:14:17: 28000000 INFO @ Wed, 28 Jun 2017 01:14:19: 28000000 INFO @ Wed, 28 Jun 2017 01:14:20: 28000000 INFO @ Wed, 28 Jun 2017 01:14:22: 29000000 INFO @ Wed, 28 Jun 2017 01:14:25: 29000000 INFO @ Wed, 28 Jun 2017 01:14:26: 29000000 INFO @ Wed, 28 Jun 2017 01:14:28: 30000000 INFO @ Wed, 28 Jun 2017 01:14:31: 30000000 INFO @ Wed, 28 Jun 2017 01:14:32: 30000000 INFO @ Wed, 28 Jun 2017 01:14:34: 31000000 INFO @ Wed, 28 Jun 2017 01:14:37: 31000000 INFO @ Wed, 28 Jun 2017 01:14:38: 31000000 INFO @ Wed, 28 Jun 2017 01:14:39: 32000000 INFO @ Wed, 28 Jun 2017 01:14:43: 32000000 INFO @ Wed, 28 Jun 2017 01:14:44: 32000000 INFO @ Wed, 28 Jun 2017 01:14:45: 33000000 INFO @ Wed, 28 Jun 2017 01:14:49: 33000000 INFO @ Wed, 28 Jun 2017 01:14:50: 33000000 INFO @ Wed, 28 Jun 2017 01:14:51: 34000000 INFO @ Wed, 28 Jun 2017 01:14:55: 34000000 INFO @ Wed, 28 Jun 2017 01:14:55: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 01:14:55: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 01:14:55: #1 total tags in treatment: 16461318 INFO @ Wed, 28 Jun 2017 01:14:55: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:14:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 01:14:56: #1 tags after filtering in treatment: 12489228 INFO @ Wed, 28 Jun 2017 01:14:56: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 28 Jun 2017 01:14:56: #1 finished! INFO @ Wed, 28 Jun 2017 01:14:56: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:14:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:14:56: 34000000 INFO @ Wed, 28 Jun 2017 01:14:57: #2 number of paired peaks: 4893 INFO @ Wed, 28 Jun 2017 01:14:57: start model_add_line... INFO @ Wed, 28 Jun 2017 01:14:57: start X-correlation... INFO @ Wed, 28 Jun 2017 01:14:57: end of X-cor INFO @ Wed, 28 Jun 2017 01:14:57: #2 finished! INFO @ Wed, 28 Jun 2017 01:14:57: #2 predicted fragment length is 190 bps INFO @ Wed, 28 Jun 2017 01:14:57: #2 alternative fragment length(s) may be 3,190 bps INFO @ Wed, 28 Jun 2017 01:14:57: #2.2 Generate R script for model : SRX749065.05_model.r INFO @ Wed, 28 Jun 2017 01:14:57: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:14:57: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:15:00: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 01:15:00: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 01:15:00: #1 total tags in treatment: 16461318 INFO @ Wed, 28 Jun 2017 01:15:00: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:15:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 01:15:00: #1 tags after filtering in treatment: 12489228 INFO @ Wed, 28 Jun 2017 01:15:00: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 28 Jun 2017 01:15:00: #1 finished! INFO @ Wed, 28 Jun 2017 01:15:00: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:15:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:15:01: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 01:15:01: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 01:15:01: #1 total tags in treatment: 16461318 INFO @ Wed, 28 Jun 2017 01:15:01: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:15:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 01:15:01: #1 tags after filtering in treatment: 12489228 INFO @ Wed, 28 Jun 2017 01:15:01: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 28 Jun 2017 01:15:01: #1 finished! INFO @ Wed, 28 Jun 2017 01:15:01: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:15:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:15:01: #2 number of paired peaks: 4893 INFO @ Wed, 28 Jun 2017 01:15:01: start model_add_line... INFO @ Wed, 28 Jun 2017 01:15:02: start X-correlation... INFO @ Wed, 28 Jun 2017 01:15:02: end of X-cor INFO @ Wed, 28 Jun 2017 01:15:02: #2 finished! INFO @ Wed, 28 Jun 2017 01:15:02: #2 predicted fragment length is 190 bps INFO @ Wed, 28 Jun 2017 01:15:02: #2 alternative fragment length(s) may be 3,190 bps INFO @ Wed, 28 Jun 2017 01:15:02: #2.2 Generate R script for model : SRX749065.10_model.r INFO @ Wed, 28 Jun 2017 01:15:02: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:15:02: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:15:02: #2 number of paired peaks: 4893 INFO @ Wed, 28 Jun 2017 01:15:02: start model_add_line... INFO @ Wed, 28 Jun 2017 01:15:03: start X-correlation... INFO @ Wed, 28 Jun 2017 01:15:03: end of X-cor INFO @ Wed, 28 Jun 2017 01:15:03: #2 finished! INFO @ Wed, 28 Jun 2017 01:15:03: #2 predicted fragment length is 190 bps INFO @ Wed, 28 Jun 2017 01:15:03: #2 alternative fragment length(s) may be 3,190 bps INFO @ Wed, 28 Jun 2017 01:15:03: #2.2 Generate R script for model : SRX749065.20_model.r INFO @ Wed, 28 Jun 2017 01:15:03: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:15:03: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:15:44: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:15:47: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:15:49: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:15:59: #4 Write output xls file... SRX749065.05_peaks.xls INFO @ Wed, 28 Jun 2017 01:15:59: #4 Write peak in narrowPeak format file... SRX749065.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:15:59: #4 Write summits bed file... SRX749065.05_summits.bed INFO @ Wed, 28 Jun 2017 01:15:59: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5331 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 01:16:03: #4 Write output xls file... SRX749065.10_peaks.xls INFO @ Wed, 28 Jun 2017 01:16:03: #4 Write peak in narrowPeak format file... SRX749065.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:16:03: #4 Write summits bed file... SRX749065.10_summits.bed INFO @ Wed, 28 Jun 2017 01:16:03: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3385 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 01:16:04: #4 Write output xls file... SRX749065.20_peaks.xls INFO @ Wed, 28 Jun 2017 01:16:04: #4 Write peak in narrowPeak format file... SRX749065.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:16:04: #4 Write summits bed file... SRX749065.20_summits.bed INFO @ Wed, 28 Jun 2017 01:16:04: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1832 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。