Job ID = 9158565 sra ファイルのダウンロード中... Completed: 476541K bytes transferred in 5 seconds (689491K 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 8414196 spots for /home/okishinya/chipatlas/results/dm3/SRX1728714/SRR3452731.sra Written 8414196 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: 00:16:45 8414196 reads; of these: 8414196 (100.00%) were paired; of these: 635160 (7.55%) aligned concordantly 0 times 6146029 (73.04%) aligned concordantly exactly 1 time 1633007 (19.41%) aligned concordantly >1 times ---- 635160 pairs aligned concordantly 0 times; of these: 145008 (22.83%) aligned discordantly 1 time ---- 490152 pairs aligned 0 times concordantly or discordantly; of these: 980304 mates make up the pairs; of these: 571107 (58.26%) aligned 0 times 269424 (27.48%) aligned exactly 1 time 139773 (14.26%) aligned >1 times 96.61% overall alignment rate Time searching: 00:16:45 Overall time: 00:16:45 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 8 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] 45418 / 7916280 = 0.0057 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, 27 Jun 2017 18:20:52: # Command line: callpeak -t SRX1728714.bam -f BAM -g dm -n SRX1728714.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1728714.20 # format = BAM # ChIP-seq file = ['SRX1728714.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 @ Tue, 27 Jun 2017 18:20:52: # Command line: callpeak -t SRX1728714.bam -f BAM -g dm -n SRX1728714.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1728714.10 # format = BAM # ChIP-seq file = ['SRX1728714.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 @ Tue, 27 Jun 2017 18:20:52: # Command line: callpeak -t SRX1728714.bam -f BAM -g dm -n SRX1728714.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1728714.05 # format = BAM # ChIP-seq file = ['SRX1728714.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 @ Tue, 27 Jun 2017 18:20:52: #1 read tag files... INFO @ Tue, 27 Jun 2017 18:20:52: #1 read tag files... INFO @ Tue, 27 Jun 2017 18:20:52: #1 read tag files... INFO @ Tue, 27 Jun 2017 18:20:52: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 18:20:52: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 18:20:52: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 18:21:00: 1000000 INFO @ Tue, 27 Jun 2017 18:21:00: 1000000 INFO @ Tue, 27 Jun 2017 18:21:00: 1000000 INFO @ Tue, 27 Jun 2017 18:21:08: 2000000 INFO @ Tue, 27 Jun 2017 18:21:08: 2000000 INFO @ Tue, 27 Jun 2017 18:21:08: 2000000 INFO @ Tue, 27 Jun 2017 18:21:16: 3000000 INFO @ Tue, 27 Jun 2017 18:21:16: 3000000 INFO @ Tue, 27 Jun 2017 18:21:17: 3000000 INFO @ Tue, 27 Jun 2017 18:21:25: 4000000 INFO @ Tue, 27 Jun 2017 18:21:25: 4000000 INFO @ Tue, 27 Jun 2017 18:21:25: 4000000 INFO @ Tue, 27 Jun 2017 18:21:33: 5000000 INFO @ Tue, 27 Jun 2017 18:21:33: 5000000 INFO @ Tue, 27 Jun 2017 18:21:34: 5000000 INFO @ Tue, 27 Jun 2017 18:21:40: 6000000 INFO @ Tue, 27 Jun 2017 18:21:40: 6000000 INFO @ Tue, 27 Jun 2017 18:21:41: 6000000 INFO @ Tue, 27 Jun 2017 18:21:47: 7000000 INFO @ Tue, 27 Jun 2017 18:21:47: 7000000 INFO @ Tue, 27 Jun 2017 18:21:47: 7000000 INFO @ Tue, 27 Jun 2017 18:21:54: 8000000 INFO @ Tue, 27 Jun 2017 18:21:54: 8000000 INFO @ Tue, 27 Jun 2017 18:21:54: 8000000 INFO @ Tue, 27 Jun 2017 18:22:00: 9000000 INFO @ Tue, 27 Jun 2017 18:22:01: 9000000 INFO @ Tue, 27 Jun 2017 18:22:01: 9000000 INFO @ Tue, 27 Jun 2017 18:22:07: 10000000 INFO @ Tue, 27 Jun 2017 18:22:08: 10000000 INFO @ Tue, 27 Jun 2017 18:22:08: 10000000 INFO @ Tue, 27 Jun 2017 18:22:13: 11000000 INFO @ Tue, 27 Jun 2017 18:22:15: 11000000 INFO @ Tue, 27 Jun 2017 18:22:15: 11000000 INFO @ Tue, 27 Jun 2017 18:22:20: 12000000 INFO @ Tue, 27 Jun 2017 18:22:23: 12000000 INFO @ Tue, 27 Jun 2017 18:22:23: 12000000 INFO @ Tue, 27 Jun 2017 18:22:27: 13000000 INFO @ Tue, 27 Jun 2017 18:22:30: 13000000 INFO @ Tue, 27 Jun 2017 18:22:30: 13000000 INFO @ Tue, 27 Jun 2017 18:22:33: 14000000 INFO @ Tue, 27 Jun 2017 18:22:37: 14000000 INFO @ Tue, 27 Jun 2017 18:22:37: 14000000 INFO @ Tue, 27 Jun 2017 18:22:40: 15000000 INFO @ Tue, 27 Jun 2017 18:22:44: 15000000 INFO @ Tue, 27 Jun 2017 18:22:44: 15000000 INFO @ Tue, 27 Jun 2017 18:22:46: 16000000 INFO @ Tue, 27 Jun 2017 18:22:47: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 18:22:47: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 18:22:47: #1 total tags in treatment: 7733994 INFO @ Tue, 27 Jun 2017 18:22:47: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 18:22:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 18:22:47: #1 tags after filtering in treatment: 7468198 INFO @ Tue, 27 Jun 2017 18:22:47: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 27 Jun 2017 18:22:47: #1 finished! INFO @ Tue, 27 Jun 2017 18:22:47: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 18:22:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 18:22:48: #2 number of paired peaks: 413 WARNING @ Tue, 27 Jun 2017 18:22:48: Fewer paired peaks (413) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 413 pairs to build model! INFO @ Tue, 27 Jun 2017 18:22:48: start model_add_line... INFO @ Tue, 27 Jun 2017 18:22:48: start X-correlation... INFO @ Tue, 27 Jun 2017 18:22:48: end of X-cor INFO @ Tue, 27 Jun 2017 18:22:48: #2 finished! INFO @ Tue, 27 Jun 2017 18:22:48: #2 predicted fragment length is 167 bps INFO @ Tue, 27 Jun 2017 18:22:48: #2 alternative fragment length(s) may be 167,183 bps INFO @ Tue, 27 Jun 2017 18:22:48: #2.2 Generate R script for model : SRX1728714.10_model.r INFO @ Tue, 27 Jun 2017 18:22:48: #3 Call peaks... INFO @ Tue, 27 Jun 2017 18:22:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 18:22:51: 16000000 INFO @ Tue, 27 Jun 2017 18:22:51: 16000000 INFO @ Tue, 27 Jun 2017 18:22:52: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 18:22:52: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 18:22:52: #1 total tags in treatment: 7733994 INFO @ Tue, 27 Jun 2017 18:22:52: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 18:22:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 18:22:52: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 18:22:52: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 18:22:52: #1 total tags in treatment: 7733994 INFO @ Tue, 27 Jun 2017 18:22:52: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 18:22:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 18:22:52: #1 tags after filtering in treatment: 7468198 INFO @ Tue, 27 Jun 2017 18:22:52: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 27 Jun 2017 18:22:52: #1 finished! INFO @ Tue, 27 Jun 2017 18:22:52: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 18:22:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 18:22:52: #1 tags after filtering in treatment: 7468198 INFO @ Tue, 27 Jun 2017 18:22:52: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 27 Jun 2017 18:22:52: #1 finished! INFO @ Tue, 27 Jun 2017 18:22:52: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 18:22:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 18:22:53: #2 number of paired peaks: 413 WARNING @ Tue, 27 Jun 2017 18:22:53: Fewer paired peaks (413) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 413 pairs to build model! INFO @ Tue, 27 Jun 2017 18:22:53: start model_add_line... INFO @ Tue, 27 Jun 2017 18:22:53: #2 number of paired peaks: 413 WARNING @ Tue, 27 Jun 2017 18:22:53: Fewer paired peaks (413) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 413 pairs to build model! INFO @ Tue, 27 Jun 2017 18:22:53: start model_add_line... INFO @ Tue, 27 Jun 2017 18:22:53: start X-correlation... INFO @ Tue, 27 Jun 2017 18:22:53: end of X-cor INFO @ Tue, 27 Jun 2017 18:22:53: #2 finished! INFO @ Tue, 27 Jun 2017 18:22:53: #2 predicted fragment length is 167 bps INFO @ Tue, 27 Jun 2017 18:22:53: #2 alternative fragment length(s) may be 167,183 bps INFO @ Tue, 27 Jun 2017 18:22:53: #2.2 Generate R script for model : SRX1728714.20_model.r INFO @ Tue, 27 Jun 2017 18:22:53: #3 Call peaks... INFO @ Tue, 27 Jun 2017 18:22:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 18:22:53: start X-correlation... INFO @ Tue, 27 Jun 2017 18:22:53: end of X-cor INFO @ Tue, 27 Jun 2017 18:22:53: #2 finished! INFO @ Tue, 27 Jun 2017 18:22:53: #2 predicted fragment length is 167 bps INFO @ Tue, 27 Jun 2017 18:22:53: #2 alternative fragment length(s) may be 167,183 bps INFO @ Tue, 27 Jun 2017 18:22:53: #2.2 Generate R script for model : SRX1728714.05_model.r INFO @ Tue, 27 Jun 2017 18:22:53: #3 Call peaks... INFO @ Tue, 27 Jun 2017 18:22:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 18:23:05: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 18:23:11: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 18:23:11: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 18:23:14: #4 Write output xls file... SRX1728714.10_peaks.xls INFO @ Tue, 27 Jun 2017 18:23:14: #4 Write peak in narrowPeak format file... SRX1728714.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 18:23:14: #4 Write summits bed file... SRX1728714.10_summits.bed INFO @ Tue, 27 Jun 2017 18:23:14: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (577 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 18:23:21: #4 Write output xls file... SRX1728714.20_peaks.xls INFO @ Tue, 27 Jun 2017 18:23:21: #4 Write peak in narrowPeak format file... SRX1728714.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 18:23:21: #4 Write summits bed file... SRX1728714.20_summits.bed INFO @ Tue, 27 Jun 2017 18:23:21: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (226 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 18:23:22: #4 Write output xls file... SRX1728714.05_peaks.xls INFO @ Tue, 27 Jun 2017 18:23:22: #4 Write peak in narrowPeak format file... SRX1728714.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 18:23:22: #4 Write summits bed file... SRX1728714.05_summits.bed INFO @ Tue, 27 Jun 2017 18:23:22: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1161 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。