Job ID = 9159801 sra ファイルのダウンロード中... Completed: 651748K bytes transferred in 7 seconds (674444K 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 10663248 spots for /home/okishinya/chipatlas/results/dm3/SRX683498/SRR1554224.sra Written 10663248 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: 00:28:14 10663248 reads; of these: 10663248 (100.00%) were paired; of these: 960530 (9.01%) aligned concordantly 0 times 7025254 (65.88%) aligned concordantly exactly 1 time 2677464 (25.11%) aligned concordantly >1 times ---- 960530 pairs aligned concordantly 0 times; of these: 60703 (6.32%) aligned discordantly 1 time ---- 899827 pairs aligned 0 times concordantly or discordantly; of these: 1799654 mates make up the pairs; of these: 1268474 (70.48%) aligned 0 times 363184 (20.18%) aligned exactly 1 time 167996 (9.33%) aligned >1 times 94.05% overall alignment rate Time searching: 00:28:14 Overall time: 00:28:14 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 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] 1263343 / 9752852 = 0.1295 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 00:20:08: # Command line: callpeak -t SRX683498.bam -f BAM -g dm -n SRX683498.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX683498.20 # format = BAM # ChIP-seq file = ['SRX683498.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 00:20:08: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:20:08: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:20:08: # Command line: callpeak -t SRX683498.bam -f BAM -g dm -n SRX683498.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX683498.05 # format = BAM # ChIP-seq file = ['SRX683498.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 00:20:08: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:20:08: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:20:08: # Command line: callpeak -t SRX683498.bam -f BAM -g dm -n SRX683498.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX683498.10 # format = BAM # ChIP-seq file = ['SRX683498.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 00:20:08: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:20:08: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:20:14: 1000000 INFO @ Wed, 28 Jun 2017 00:20:14: 1000000 INFO @ Wed, 28 Jun 2017 00:20:14: 1000000 INFO @ Wed, 28 Jun 2017 00:20:21: 2000000 INFO @ Wed, 28 Jun 2017 00:20:21: 2000000 INFO @ Wed, 28 Jun 2017 00:20:21: 2000000 INFO @ Wed, 28 Jun 2017 00:20:27: 3000000 INFO @ Wed, 28 Jun 2017 00:20:28: 3000000 INFO @ Wed, 28 Jun 2017 00:20:28: 3000000 INFO @ Wed, 28 Jun 2017 00:20:33: 4000000 INFO @ Wed, 28 Jun 2017 00:20:35: 4000000 INFO @ Wed, 28 Jun 2017 00:20:35: 4000000 INFO @ Wed, 28 Jun 2017 00:20:39: 5000000 INFO @ Wed, 28 Jun 2017 00:20:42: 5000000 INFO @ Wed, 28 Jun 2017 00:20:42: 5000000 INFO @ Wed, 28 Jun 2017 00:20:46: 6000000 INFO @ Wed, 28 Jun 2017 00:20:49: 6000000 INFO @ Wed, 28 Jun 2017 00:20:49: 6000000 INFO @ Wed, 28 Jun 2017 00:20:52: 7000000 INFO @ Wed, 28 Jun 2017 00:20:55: 7000000 INFO @ Wed, 28 Jun 2017 00:20:56: 7000000 INFO @ Wed, 28 Jun 2017 00:20:58: 8000000 INFO @ Wed, 28 Jun 2017 00:21:02: 8000000 INFO @ Wed, 28 Jun 2017 00:21:02: 8000000 INFO @ Wed, 28 Jun 2017 00:21:04: 9000000 INFO @ Wed, 28 Jun 2017 00:21:09: 9000000 INFO @ Wed, 28 Jun 2017 00:21:09: 9000000 INFO @ Wed, 28 Jun 2017 00:21:11: 10000000 INFO @ Wed, 28 Jun 2017 00:21:16: 10000000 INFO @ Wed, 28 Jun 2017 00:21:16: 10000000 INFO @ Wed, 28 Jun 2017 00:21:17: 11000000 INFO @ Wed, 28 Jun 2017 00:21:22: 11000000 INFO @ Wed, 28 Jun 2017 00:21:23: 11000000 INFO @ Wed, 28 Jun 2017 00:21:24: 12000000 INFO @ Wed, 28 Jun 2017 00:21:29: 12000000 INFO @ Wed, 28 Jun 2017 00:21:30: 13000000 INFO @ Wed, 28 Jun 2017 00:21:30: 12000000 INFO @ Wed, 28 Jun 2017 00:21:35: 13000000 INFO @ Wed, 28 Jun 2017 00:21:37: 14000000 INFO @ Wed, 28 Jun 2017 00:21:37: 13000000 INFO @ Wed, 28 Jun 2017 00:21:42: 14000000 INFO @ Wed, 28 Jun 2017 00:21:43: 15000000 INFO @ Wed, 28 Jun 2017 00:21:44: 14000000 INFO @ Wed, 28 Jun 2017 00:21:48: 15000000 INFO @ Wed, 28 Jun 2017 00:21:49: 16000000 INFO @ Wed, 28 Jun 2017 00:21:51: 15000000 INFO @ Wed, 28 Jun 2017 00:21:55: 16000000 INFO @ Wed, 28 Jun 2017 00:21:56: 17000000 INFO @ Wed, 28 Jun 2017 00:21:58: 16000000 INFO @ Wed, 28 Jun 2017 00:21:59: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:21:59: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:21:59: #1 total tags in treatment: 8442502 INFO @ Wed, 28 Jun 2017 00:21:59: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:21:59: #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 00:22:00: #1 tags after filtering in treatment: 8098612 INFO @ Wed, 28 Jun 2017 00:22:00: #1 Redundant rate of treatment: 0.04 INFO @ Wed, 28 Jun 2017 00:22:00: #1 finished! INFO @ Wed, 28 Jun 2017 00:22:00: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:22:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:22:00: #2 number of paired peaks: 326 WARNING @ Wed, 28 Jun 2017 00:22:00: Fewer paired peaks (326) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 326 pairs to build model! INFO @ Wed, 28 Jun 2017 00:22:00: start model_add_line... INFO @ Wed, 28 Jun 2017 00:22:00: start X-correlation... INFO @ Wed, 28 Jun 2017 00:22:00: end of X-cor INFO @ Wed, 28 Jun 2017 00:22:00: #2 finished! INFO @ Wed, 28 Jun 2017 00:22:00: #2 predicted fragment length is 135 bps INFO @ Wed, 28 Jun 2017 00:22:00: #2 alternative fragment length(s) may be 135 bps INFO @ Wed, 28 Jun 2017 00:22:00: #2.2 Generate R script for model : SRX683498.10_model.r INFO @ Wed, 28 Jun 2017 00:22:00: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:22:00: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:22:01: 17000000 INFO @ Wed, 28 Jun 2017 00:22:04: 17000000 INFO @ Wed, 28 Jun 2017 00:22:05: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:22:05: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:22:05: #1 total tags in treatment: 8442502 INFO @ Wed, 28 Jun 2017 00:22:05: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:22:05: #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 00:22:05: #1 tags after filtering in treatment: 8098612 INFO @ Wed, 28 Jun 2017 00:22:05: #1 Redundant rate of treatment: 0.04 INFO @ Wed, 28 Jun 2017 00:22:05: #1 finished! INFO @ Wed, 28 Jun 2017 00:22:05: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:22:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:22:06: #2 number of paired peaks: 326 WARNING @ Wed, 28 Jun 2017 00:22:06: Fewer paired peaks (326) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 326 pairs to build model! INFO @ Wed, 28 Jun 2017 00:22:06: start model_add_line... INFO @ Wed, 28 Jun 2017 00:22:06: start X-correlation... INFO @ Wed, 28 Jun 2017 00:22:06: end of X-cor INFO @ Wed, 28 Jun 2017 00:22:06: #2 finished! INFO @ Wed, 28 Jun 2017 00:22:06: #2 predicted fragment length is 135 bps INFO @ Wed, 28 Jun 2017 00:22:06: #2 alternative fragment length(s) may be 135 bps INFO @ Wed, 28 Jun 2017 00:22:06: #2.2 Generate R script for model : SRX683498.20_model.r INFO @ Wed, 28 Jun 2017 00:22:06: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:22:06: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:22:08: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:22:08: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:22:08: #1 total tags in treatment: 8442502 INFO @ Wed, 28 Jun 2017 00:22:08: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:22:08: #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 00:22:08: #1 tags after filtering in treatment: 8098612 INFO @ Wed, 28 Jun 2017 00:22:08: #1 Redundant rate of treatment: 0.04 INFO @ Wed, 28 Jun 2017 00:22:08: #1 finished! INFO @ Wed, 28 Jun 2017 00:22:08: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:22:08: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:22:08: #2 number of paired peaks: 326 WARNING @ Wed, 28 Jun 2017 00:22:08: Fewer paired peaks (326) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 326 pairs to build model! INFO @ Wed, 28 Jun 2017 00:22:08: start model_add_line... INFO @ Wed, 28 Jun 2017 00:22:08: start X-correlation... INFO @ Wed, 28 Jun 2017 00:22:08: end of X-cor INFO @ Wed, 28 Jun 2017 00:22:08: #2 finished! INFO @ Wed, 28 Jun 2017 00:22:08: #2 predicted fragment length is 135 bps INFO @ Wed, 28 Jun 2017 00:22:08: #2 alternative fragment length(s) may be 135 bps INFO @ Wed, 28 Jun 2017 00:22:08: #2.2 Generate R script for model : SRX683498.05_model.r INFO @ Wed, 28 Jun 2017 00:22:08: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:22:08: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:22:18: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:22:25: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:22:28: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:22:28: #4 Write output xls file... SRX683498.10_peaks.xls INFO @ Wed, 28 Jun 2017 00:22:28: #4 Write peak in narrowPeak format file... SRX683498.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:22:28: #4 Write summits bed file... SRX683498.10_summits.bed INFO @ Wed, 28 Jun 2017 00:22:28: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (824 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 00:22:34: #4 Write output xls file... SRX683498.20_peaks.xls INFO @ Wed, 28 Jun 2017 00:22:34: #4 Write peak in narrowPeak format file... SRX683498.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:22:34: #4 Write summits bed file... SRX683498.20_summits.bed INFO @ Wed, 28 Jun 2017 00:22:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (515 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 00:22:37: #4 Write output xls file... SRX683498.05_peaks.xls INFO @ Wed, 28 Jun 2017 00:22:37: #4 Write peak in narrowPeak format file... SRX683498.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:22:37: #4 Write summits bed file... SRX683498.05_summits.bed INFO @ Wed, 28 Jun 2017 00:22:37: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1446 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。