Job ID = 9159868 sra ファイルのダウンロード中... Completed: 1305978K bytes transferred in 14 seconds (757200K 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 20050169 spots for /home/okishinya/chipatlas/results/dm3/SRX749075/SRR1636803.sra Written 20050169 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: 00:43:14 20050169 reads; of these: 20050169 (100.00%) were paired; of these: 2029984 (10.12%) aligned concordantly 0 times 14070827 (70.18%) aligned concordantly exactly 1 time 3949358 (19.70%) aligned concordantly >1 times ---- 2029984 pairs aligned concordantly 0 times; of these: 8560 (0.42%) aligned discordantly 1 time ---- 2021424 pairs aligned 0 times concordantly or discordantly; of these: 4042848 mates make up the pairs; of these: 3629454 (89.77%) aligned 0 times 316945 (7.84%) aligned exactly 1 time 96449 (2.39%) aligned >1 times 90.95% overall alignment rate Time searching: 00:43:14 Overall time: 00:43:14 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] 3437190 / 18014883 = 0.1908 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 01:21:52: # Command line: callpeak -t SRX749075.bam -f BAM -g dm -n SRX749075.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX749075.10 # format = BAM # ChIP-seq file = ['SRX749075.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 01:21:52: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:21:52: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:21:52: # Command line: callpeak -t SRX749075.bam -f BAM -g dm -n SRX749075.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX749075.05 # format = BAM # ChIP-seq file = ['SRX749075.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 01:21:52: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:21:52: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:21:52: # Command line: callpeak -t SRX749075.bam -f BAM -g dm -n SRX749075.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX749075.20 # format = BAM # ChIP-seq file = ['SRX749075.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 01:21:52: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:21:52: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:21:59: 1000000 INFO @ Wed, 28 Jun 2017 01:21:59: 1000000 INFO @ Wed, 28 Jun 2017 01:21:59: 1000000 INFO @ Wed, 28 Jun 2017 01:22:06: 2000000 INFO @ Wed, 28 Jun 2017 01:22:06: 2000000 INFO @ Wed, 28 Jun 2017 01:22:06: 2000000 INFO @ Wed, 28 Jun 2017 01:22:13: 3000000 INFO @ Wed, 28 Jun 2017 01:22:13: 3000000 INFO @ Wed, 28 Jun 2017 01:22:13: 3000000 INFO @ Wed, 28 Jun 2017 01:22:20: 4000000 INFO @ Wed, 28 Jun 2017 01:22:20: 4000000 INFO @ Wed, 28 Jun 2017 01:22:20: 4000000 INFO @ Wed, 28 Jun 2017 01:22:27: 5000000 INFO @ Wed, 28 Jun 2017 01:22:27: 5000000 INFO @ Wed, 28 Jun 2017 01:22:27: 5000000 INFO @ Wed, 28 Jun 2017 01:22:34: 6000000 INFO @ Wed, 28 Jun 2017 01:22:34: 6000000 INFO @ Wed, 28 Jun 2017 01:22:34: 6000000 INFO @ Wed, 28 Jun 2017 01:22:41: 7000000 INFO @ Wed, 28 Jun 2017 01:22:41: 7000000 INFO @ Wed, 28 Jun 2017 01:22:41: 7000000 INFO @ Wed, 28 Jun 2017 01:22:49: 8000000 INFO @ Wed, 28 Jun 2017 01:22:49: 8000000 INFO @ Wed, 28 Jun 2017 01:22:49: 8000000 INFO @ Wed, 28 Jun 2017 01:22:56: 9000000 INFO @ Wed, 28 Jun 2017 01:22:56: 9000000 INFO @ Wed, 28 Jun 2017 01:22:56: 9000000 INFO @ Wed, 28 Jun 2017 01:23:03: 10000000 INFO @ Wed, 28 Jun 2017 01:23:03: 10000000 INFO @ Wed, 28 Jun 2017 01:23:03: 10000000 INFO @ Wed, 28 Jun 2017 01:23:11: 11000000 INFO @ Wed, 28 Jun 2017 01:23:11: 11000000 INFO @ Wed, 28 Jun 2017 01:23:11: 11000000 INFO @ Wed, 28 Jun 2017 01:23:18: 12000000 INFO @ Wed, 28 Jun 2017 01:23:18: 12000000 INFO @ Wed, 28 Jun 2017 01:23:18: 12000000 INFO @ Wed, 28 Jun 2017 01:23:25: 13000000 INFO @ Wed, 28 Jun 2017 01:23:25: 13000000 INFO @ Wed, 28 Jun 2017 01:23:25: 13000000 INFO @ Wed, 28 Jun 2017 01:23:32: 14000000 INFO @ Wed, 28 Jun 2017 01:23:32: 14000000 INFO @ Wed, 28 Jun 2017 01:23:32: 14000000 INFO @ Wed, 28 Jun 2017 01:23:39: 15000000 INFO @ Wed, 28 Jun 2017 01:23:39: 15000000 INFO @ Wed, 28 Jun 2017 01:23:39: 15000000 INFO @ Wed, 28 Jun 2017 01:23:46: 16000000 INFO @ Wed, 28 Jun 2017 01:23:46: 16000000 INFO @ Wed, 28 Jun 2017 01:23:46: 16000000 INFO @ Wed, 28 Jun 2017 01:23:53: 17000000 INFO @ Wed, 28 Jun 2017 01:23:53: 17000000 INFO @ Wed, 28 Jun 2017 01:23:53: 17000000 INFO @ Wed, 28 Jun 2017 01:24:00: 18000000 INFO @ Wed, 28 Jun 2017 01:24:00: 18000000 INFO @ Wed, 28 Jun 2017 01:24:00: 18000000 INFO @ Wed, 28 Jun 2017 01:24:07: 19000000 INFO @ Wed, 28 Jun 2017 01:24:07: 19000000 INFO @ Wed, 28 Jun 2017 01:24:08: 19000000 INFO @ Wed, 28 Jun 2017 01:24:14: 20000000 INFO @ Wed, 28 Jun 2017 01:24:14: 20000000 INFO @ Wed, 28 Jun 2017 01:24:15: 20000000 INFO @ Wed, 28 Jun 2017 01:24:22: 21000000 INFO @ Wed, 28 Jun 2017 01:24:22: 21000000 INFO @ Wed, 28 Jun 2017 01:24:23: 21000000 INFO @ Wed, 28 Jun 2017 01:24:29: 22000000 INFO @ Wed, 28 Jun 2017 01:24:29: 22000000 INFO @ Wed, 28 Jun 2017 01:24:31: 22000000 INFO @ Wed, 28 Jun 2017 01:24:37: 23000000 INFO @ Wed, 28 Jun 2017 01:24:37: 23000000 INFO @ Wed, 28 Jun 2017 01:24:38: 23000000 INFO @ Wed, 28 Jun 2017 01:24:44: 24000000 INFO @ Wed, 28 Jun 2017 01:24:44: 24000000 INFO @ Wed, 28 Jun 2017 01:24:46: 24000000 INFO @ Wed, 28 Jun 2017 01:24:52: 25000000 INFO @ Wed, 28 Jun 2017 01:24:52: 25000000 INFO @ Wed, 28 Jun 2017 01:24:54: 25000000 INFO @ Wed, 28 Jun 2017 01:25:00: 26000000 INFO @ Wed, 28 Jun 2017 01:25:00: 26000000 INFO @ Wed, 28 Jun 2017 01:25:02: 26000000 INFO @ Wed, 28 Jun 2017 01:25:07: 27000000 INFO @ Wed, 28 Jun 2017 01:25:07: 27000000 INFO @ Wed, 28 Jun 2017 01:25:09: 27000000 INFO @ Wed, 28 Jun 2017 01:25:15: 28000000 INFO @ Wed, 28 Jun 2017 01:25:15: 28000000 INFO @ Wed, 28 Jun 2017 01:25:17: 28000000 INFO @ Wed, 28 Jun 2017 01:25:22: 29000000 INFO @ Wed, 28 Jun 2017 01:25:22: 29000000 INFO @ Wed, 28 Jun 2017 01:25:24: 29000000 INFO @ Wed, 28 Jun 2017 01:25:26: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 01:25:26: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 01:25:26: #1 total tags in treatment: 14583855 INFO @ Wed, 28 Jun 2017 01:25:26: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:25:26: #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 01:25:26: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 01:25:26: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 01:25:26: #1 total tags in treatment: 14583855 INFO @ Wed, 28 Jun 2017 01:25:26: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:25:26: #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 01:25:27: #1 tags after filtering in treatment: 12950580 INFO @ Wed, 28 Jun 2017 01:25:27: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 28 Jun 2017 01:25:27: #1 finished! INFO @ Wed, 28 Jun 2017 01:25:27: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:25:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:25:27: #1 tags after filtering in treatment: 12950580 INFO @ Wed, 28 Jun 2017 01:25:27: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 28 Jun 2017 01:25:27: #1 finished! INFO @ Wed, 28 Jun 2017 01:25:27: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:25:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:25:28: #2 number of paired peaks: 1154 INFO @ Wed, 28 Jun 2017 01:25:28: start model_add_line... INFO @ Wed, 28 Jun 2017 01:25:28: #2 number of paired peaks: 1154 INFO @ Wed, 28 Jun 2017 01:25:28: start model_add_line... INFO @ Wed, 28 Jun 2017 01:25:28: start X-correlation... INFO @ Wed, 28 Jun 2017 01:25:28: end of X-cor INFO @ Wed, 28 Jun 2017 01:25:28: #2 finished! INFO @ Wed, 28 Jun 2017 01:25:28: #2 predicted fragment length is 119 bps INFO @ Wed, 28 Jun 2017 01:25:28: #2 alternative fragment length(s) may be 119 bps INFO @ Wed, 28 Jun 2017 01:25:28: #2.2 Generate R script for model : SRX749075.20_model.r INFO @ Wed, 28 Jun 2017 01:25:28: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:25:28: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:25:28: start X-correlation... INFO @ Wed, 28 Jun 2017 01:25:28: end of X-cor INFO @ Wed, 28 Jun 2017 01:25:28: #2 finished! INFO @ Wed, 28 Jun 2017 01:25:28: #2 predicted fragment length is 119 bps INFO @ Wed, 28 Jun 2017 01:25:28: #2 alternative fragment length(s) may be 119 bps INFO @ Wed, 28 Jun 2017 01:25:28: #2.2 Generate R script for model : SRX749075.10_model.r INFO @ Wed, 28 Jun 2017 01:25:28: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:25:28: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:25:28: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 01:25:28: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 01:25:28: #1 total tags in treatment: 14583855 INFO @ Wed, 28 Jun 2017 01:25:28: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:25:28: #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 01:25:29: #1 tags after filtering in treatment: 12950580 INFO @ Wed, 28 Jun 2017 01:25:29: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 28 Jun 2017 01:25:29: #1 finished! INFO @ Wed, 28 Jun 2017 01:25:29: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:25:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:25:30: #2 number of paired peaks: 1154 INFO @ Wed, 28 Jun 2017 01:25:30: start model_add_line... INFO @ Wed, 28 Jun 2017 01:25:30: start X-correlation... INFO @ Wed, 28 Jun 2017 01:25:30: end of X-cor INFO @ Wed, 28 Jun 2017 01:25:30: #2 finished! INFO @ Wed, 28 Jun 2017 01:25:30: #2 predicted fragment length is 119 bps INFO @ Wed, 28 Jun 2017 01:25:30: #2 alternative fragment length(s) may be 119 bps INFO @ Wed, 28 Jun 2017 01:25:30: #2.2 Generate R script for model : SRX749075.05_model.r INFO @ Wed, 28 Jun 2017 01:25:30: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:25:30: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:25:58: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:25:59: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:26:00: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:26:15: #4 Write output xls file... SRX749075.10_peaks.xls INFO @ Wed, 28 Jun 2017 01:26:15: #4 Write peak in narrowPeak format file... SRX749075.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:26:15: #4 Write summits bed file... SRX749075.10_summits.bed INFO @ Wed, 28 Jun 2017 01:26:15: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (9183 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 01:26:15: #4 Write output xls file... SRX749075.20_peaks.xls INFO @ Wed, 28 Jun 2017 01:26:15: #4 Write peak in narrowPeak format file... SRX749075.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:26:15: #4 Write summits bed file... SRX749075.20_summits.bed INFO @ Wed, 28 Jun 2017 01:26:15: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5144 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 01:26:17: #4 Write output xls file... SRX749075.05_peaks.xls INFO @ Wed, 28 Jun 2017 01:26:17: #4 Write peak in narrowPeak format file... SRX749075.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:26:17: #4 Write summits bed file... SRX749075.05_summits.bed INFO @ Wed, 28 Jun 2017 01:26:17: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (13644 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。