Job ID = 9159853 sra ファイルのダウンロード中... Completed: 863017K bytes transferred in 10 seconds (665124K 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 13470476 spots for /home/okishinya/chipatlas/results/dm3/SRX749048/SRR1636776.sra Written 13470476 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: 00:30:21 13470476 reads; of these: 13470476 (100.00%) were paired; of these: 1263134 (9.38%) aligned concordantly 0 times 9703488 (72.04%) aligned concordantly exactly 1 time 2503854 (18.59%) aligned concordantly >1 times ---- 1263134 pairs aligned concordantly 0 times; of these: 443102 (35.08%) aligned discordantly 1 time ---- 820032 pairs aligned 0 times concordantly or discordantly; of these: 1640064 mates make up the pairs; of these: 823060 (50.18%) aligned 0 times 460769 (28.09%) aligned exactly 1 time 356235 (21.72%) aligned >1 times 96.94% overall alignment rate Time searching: 00:30:21 Overall time: 00:30:21 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 12 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] 110616 / 12642721 = 0.0087 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 00:58:19: # Command line: callpeak -t SRX749048.bam -f BAM -g dm -n SRX749048.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX749048.05 # format = BAM # ChIP-seq file = ['SRX749048.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 00:58:19: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:58:19: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:58:19: # Command line: callpeak -t SRX749048.bam -f BAM -g dm -n SRX749048.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX749048.20 # format = BAM # ChIP-seq file = ['SRX749048.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 00:58:19: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:58:19: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:58:19: # Command line: callpeak -t SRX749048.bam -f BAM -g dm -n SRX749048.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX749048.10 # format = BAM # ChIP-seq file = ['SRX749048.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 00:58:19: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:58:19: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:58:26: 1000000 INFO @ Wed, 28 Jun 2017 00:58:27: 1000000 INFO @ Wed, 28 Jun 2017 00:58:27: 1000000 INFO @ Wed, 28 Jun 2017 00:58:34: 2000000 INFO @ Wed, 28 Jun 2017 00:58:34: 2000000 INFO @ Wed, 28 Jun 2017 00:58:34: 2000000 INFO @ Wed, 28 Jun 2017 00:58:42: 3000000 INFO @ Wed, 28 Jun 2017 00:58:42: 3000000 INFO @ Wed, 28 Jun 2017 00:58:42: 3000000 INFO @ Wed, 28 Jun 2017 00:58:49: 4000000 INFO @ Wed, 28 Jun 2017 00:58:50: 4000000 INFO @ Wed, 28 Jun 2017 00:58:50: 4000000 INFO @ Wed, 28 Jun 2017 00:58:57: 5000000 INFO @ Wed, 28 Jun 2017 00:58:58: 5000000 INFO @ Wed, 28 Jun 2017 00:58:58: 5000000 INFO @ Wed, 28 Jun 2017 00:59:05: 6000000 INFO @ Wed, 28 Jun 2017 00:59:06: 6000000 INFO @ Wed, 28 Jun 2017 00:59:06: 6000000 INFO @ Wed, 28 Jun 2017 00:59:13: 7000000 INFO @ Wed, 28 Jun 2017 00:59:14: 7000000 INFO @ Wed, 28 Jun 2017 00:59:14: 7000000 INFO @ Wed, 28 Jun 2017 00:59:20: 8000000 INFO @ Wed, 28 Jun 2017 00:59:22: 8000000 INFO @ Wed, 28 Jun 2017 00:59:22: 8000000 INFO @ Wed, 28 Jun 2017 00:59:28: 9000000 INFO @ Wed, 28 Jun 2017 00:59:30: 9000000 INFO @ Wed, 28 Jun 2017 00:59:30: 9000000 INFO @ Wed, 28 Jun 2017 00:59:36: 10000000 INFO @ Wed, 28 Jun 2017 00:59:37: 10000000 INFO @ Wed, 28 Jun 2017 00:59:37: 10000000 INFO @ Wed, 28 Jun 2017 00:59:44: 11000000 INFO @ Wed, 28 Jun 2017 00:59:45: 11000000 INFO @ Wed, 28 Jun 2017 00:59:45: 11000000 INFO @ Wed, 28 Jun 2017 00:59:51: 12000000 INFO @ Wed, 28 Jun 2017 00:59:53: 12000000 INFO @ Wed, 28 Jun 2017 00:59:53: 12000000 INFO @ Wed, 28 Jun 2017 00:59:59: 13000000 INFO @ Wed, 28 Jun 2017 01:00:01: 13000000 INFO @ Wed, 28 Jun 2017 01:00:01: 13000000 INFO @ Wed, 28 Jun 2017 01:00:07: 14000000 INFO @ Wed, 28 Jun 2017 01:00:09: 14000000 INFO @ Wed, 28 Jun 2017 01:00:09: 14000000 INFO @ Wed, 28 Jun 2017 01:00:15: 15000000 INFO @ Wed, 28 Jun 2017 01:00:16: 15000000 INFO @ Wed, 28 Jun 2017 01:00:16: 15000000 INFO @ Wed, 28 Jun 2017 01:00:22: 16000000 INFO @ Wed, 28 Jun 2017 01:00:24: 16000000 INFO @ Wed, 28 Jun 2017 01:00:24: 16000000 INFO @ Wed, 28 Jun 2017 01:00:30: 17000000 INFO @ Wed, 28 Jun 2017 01:00:32: 17000000 INFO @ Wed, 28 Jun 2017 01:00:32: 17000000 INFO @ Wed, 28 Jun 2017 01:00:38: 18000000 INFO @ Wed, 28 Jun 2017 01:00:40: 18000000 INFO @ Wed, 28 Jun 2017 01:00:40: 18000000 INFO @ Wed, 28 Jun 2017 01:00:46: 19000000 INFO @ Wed, 28 Jun 2017 01:00:48: 19000000 INFO @ Wed, 28 Jun 2017 01:00:48: 19000000 INFO @ Wed, 28 Jun 2017 01:00:54: 20000000 INFO @ Wed, 28 Jun 2017 01:00:56: 20000000 INFO @ Wed, 28 Jun 2017 01:00:56: 20000000 INFO @ Wed, 28 Jun 2017 01:01:01: 21000000 INFO @ Wed, 28 Jun 2017 01:01:03: 21000000 INFO @ Wed, 28 Jun 2017 01:01:03: 21000000 INFO @ Wed, 28 Jun 2017 01:01:09: 22000000 INFO @ Wed, 28 Jun 2017 01:01:11: 22000000 INFO @ Wed, 28 Jun 2017 01:01:11: 22000000 INFO @ Wed, 28 Jun 2017 01:01:17: 23000000 INFO @ Wed, 28 Jun 2017 01:01:19: 23000000 INFO @ Wed, 28 Jun 2017 01:01:19: 23000000 INFO @ Wed, 28 Jun 2017 01:01:25: 24000000 INFO @ Wed, 28 Jun 2017 01:01:26: 24000000 INFO @ Wed, 28 Jun 2017 01:01:26: 24000000 INFO @ Wed, 28 Jun 2017 01:01:33: 25000000 INFO @ Wed, 28 Jun 2017 01:01:34: 25000000 INFO @ Wed, 28 Jun 2017 01:01:34: 25000000 INFO @ Wed, 28 Jun 2017 01:01:40: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 01:01:40: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 01:01:40: #1 total tags in treatment: 12097628 INFO @ Wed, 28 Jun 2017 01:01:40: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:01:40: #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 01:01:40: #1 tags after filtering in treatment: 11405153 INFO @ Wed, 28 Jun 2017 01:01:40: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 28 Jun 2017 01:01:40: #1 finished! INFO @ Wed, 28 Jun 2017 01:01:40: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:01:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:01:41: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 01:01:41: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 01:01:41: #1 total tags in treatment: 12097628 INFO @ Wed, 28 Jun 2017 01:01:41: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:01:41: #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 01:01:41: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 01:01:41: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 01:01:41: #1 total tags in treatment: 12097628 INFO @ Wed, 28 Jun 2017 01:01:41: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:01:41: #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 01:01:41: #1 tags after filtering in treatment: 11405153 INFO @ Wed, 28 Jun 2017 01:01:41: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 28 Jun 2017 01:01:41: #1 finished! INFO @ Wed, 28 Jun 2017 01:01:41: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:01:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:01:41: #1 tags after filtering in treatment: 11405153 INFO @ Wed, 28 Jun 2017 01:01:41: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 28 Jun 2017 01:01:41: #1 finished! INFO @ Wed, 28 Jun 2017 01:01:41: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:01:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:01:41: #2 number of paired peaks: 820 WARNING @ Wed, 28 Jun 2017 01:01:41: Fewer paired peaks (820) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 820 pairs to build model! INFO @ Wed, 28 Jun 2017 01:01:41: start model_add_line... INFO @ Wed, 28 Jun 2017 01:01:41: start X-correlation... INFO @ Wed, 28 Jun 2017 01:01:41: end of X-cor INFO @ Wed, 28 Jun 2017 01:01:41: #2 finished! INFO @ Wed, 28 Jun 2017 01:01:41: #2 predicted fragment length is 199 bps INFO @ Wed, 28 Jun 2017 01:01:41: #2 alternative fragment length(s) may be 4,199 bps INFO @ Wed, 28 Jun 2017 01:01:41: #2.2 Generate R script for model : SRX749048.05_model.r INFO @ Wed, 28 Jun 2017 01:01:41: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:01:41: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:01:42: #2 number of paired peaks: 820 WARNING @ Wed, 28 Jun 2017 01:01:42: Fewer paired peaks (820) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 820 pairs to build model! INFO @ Wed, 28 Jun 2017 01:01:42: start model_add_line... INFO @ Wed, 28 Jun 2017 01:01:42: #2 number of paired peaks: 820 WARNING @ Wed, 28 Jun 2017 01:01:42: Fewer paired peaks (820) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 820 pairs to build model! INFO @ Wed, 28 Jun 2017 01:01:42: start model_add_line... INFO @ Wed, 28 Jun 2017 01:01:42: start X-correlation... INFO @ Wed, 28 Jun 2017 01:01:42: end of X-cor INFO @ Wed, 28 Jun 2017 01:01:42: #2 finished! INFO @ Wed, 28 Jun 2017 01:01:42: #2 predicted fragment length is 199 bps INFO @ Wed, 28 Jun 2017 01:01:42: #2 alternative fragment length(s) may be 4,199 bps INFO @ Wed, 28 Jun 2017 01:01:42: #2.2 Generate R script for model : SRX749048.20_model.r INFO @ Wed, 28 Jun 2017 01:01:42: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:01:42: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:01:42: start X-correlation... INFO @ Wed, 28 Jun 2017 01:01:42: end of X-cor INFO @ Wed, 28 Jun 2017 01:01:42: #2 finished! INFO @ Wed, 28 Jun 2017 01:01:42: #2 predicted fragment length is 199 bps INFO @ Wed, 28 Jun 2017 01:01:42: #2 alternative fragment length(s) may be 4,199 bps INFO @ Wed, 28 Jun 2017 01:01:42: #2.2 Generate R script for model : SRX749048.10_model.r INFO @ Wed, 28 Jun 2017 01:01:42: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:01:42: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:02:09: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:02:11: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:02:13: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:02:26: #4 Write output xls file... SRX749048.20_peaks.xls INFO @ Wed, 28 Jun 2017 01:02:26: #4 Write peak in narrowPeak format file... SRX749048.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:02:26: #4 Write summits bed file... SRX749048.20_summits.bed INFO @ Wed, 28 Jun 2017 01:02:26: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (640 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 01:02:27: #4 Write output xls file... SRX749048.05_peaks.xls INFO @ Wed, 28 Jun 2017 01:02:27: #4 Write peak in narrowPeak format file... SRX749048.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:02:27: #4 Write summits bed file... SRX749048.05_summits.bed INFO @ Wed, 28 Jun 2017 01:02:27: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5927 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 01:02:29: #4 Write output xls file... SRX749048.10_peaks.xls INFO @ Wed, 28 Jun 2017 01:02:29: #4 Write peak in narrowPeak format file... SRX749048.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:02:29: #4 Write summits bed file... SRX749048.10_summits.bed INFO @ Wed, 28 Jun 2017 01:02:29: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2089 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。