Job ID = 9159865 sra ファイルのダウンロード中... Completed: 531028K bytes transferred in 7 seconds (607238K 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 9640641 spots for /home/okishinya/chipatlas/results/dm3/SRX749070/SRR1636798.sra Written 9640641 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: 00:27:03 9640641 reads; of these: 9640641 (100.00%) were paired; of these: 671890 (6.97%) aligned concordantly 0 times 6771378 (70.24%) aligned concordantly exactly 1 time 2197373 (22.79%) aligned concordantly >1 times ---- 671890 pairs aligned concordantly 0 times; of these: 8020 (1.19%) aligned discordantly 1 time ---- 663870 pairs aligned 0 times concordantly or discordantly; of these: 1327740 mates make up the pairs; of these: 1099434 (82.80%) aligned 0 times 150946 (11.37%) aligned exactly 1 time 77360 (5.83%) aligned >1 times 94.30% overall alignment rate Time searching: 00:27:03 Overall time: 00:27:03 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] 1780521 / 8970332 = 0.1985 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 00:55:49: # Command line: callpeak -t SRX749070.bam -f BAM -g dm -n SRX749070.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX749070.10 # format = BAM # ChIP-seq file = ['SRX749070.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 00:55:49: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:55:49: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:55:49: # Command line: callpeak -t SRX749070.bam -f BAM -g dm -n SRX749070.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX749070.20 # format = BAM # ChIP-seq file = ['SRX749070.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 00:55:49: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:55:49: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:55:49: # Command line: callpeak -t SRX749070.bam -f BAM -g dm -n SRX749070.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX749070.05 # format = BAM # ChIP-seq file = ['SRX749070.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 00:55:49: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:55:49: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:55:54: 1000000 INFO @ Wed, 28 Jun 2017 00:55:54: 1000000 INFO @ Wed, 28 Jun 2017 00:55:54: 1000000 INFO @ Wed, 28 Jun 2017 00:56:00: 2000000 INFO @ Wed, 28 Jun 2017 00:56:00: 2000000 INFO @ Wed, 28 Jun 2017 00:56:00: 2000000 INFO @ Wed, 28 Jun 2017 00:56:05: 3000000 INFO @ Wed, 28 Jun 2017 00:56:05: 3000000 INFO @ Wed, 28 Jun 2017 00:56:06: 3000000 INFO @ Wed, 28 Jun 2017 00:56:11: 4000000 INFO @ Wed, 28 Jun 2017 00:56:11: 4000000 INFO @ Wed, 28 Jun 2017 00:56:12: 4000000 INFO @ Wed, 28 Jun 2017 00:56:17: 5000000 INFO @ Wed, 28 Jun 2017 00:56:17: 5000000 INFO @ Wed, 28 Jun 2017 00:56:18: 5000000 INFO @ Wed, 28 Jun 2017 00:56:23: 6000000 INFO @ Wed, 28 Jun 2017 00:56:23: 6000000 INFO @ Wed, 28 Jun 2017 00:56:24: 6000000 INFO @ Wed, 28 Jun 2017 00:56:29: 7000000 INFO @ Wed, 28 Jun 2017 00:56:29: 7000000 INFO @ Wed, 28 Jun 2017 00:56:30: 7000000 INFO @ Wed, 28 Jun 2017 00:56:35: 8000000 INFO @ Wed, 28 Jun 2017 00:56:35: 8000000 INFO @ Wed, 28 Jun 2017 00:56:37: 8000000 INFO @ Wed, 28 Jun 2017 00:56:40: 9000000 INFO @ Wed, 28 Jun 2017 00:56:40: 9000000 INFO @ Wed, 28 Jun 2017 00:56:42: 9000000 INFO @ Wed, 28 Jun 2017 00:56:46: 10000000 INFO @ Wed, 28 Jun 2017 00:56:46: 10000000 INFO @ Wed, 28 Jun 2017 00:56:48: 10000000 INFO @ Wed, 28 Jun 2017 00:56:51: 11000000 INFO @ Wed, 28 Jun 2017 00:56:52: 11000000 INFO @ Wed, 28 Jun 2017 00:56:54: 11000000 INFO @ Wed, 28 Jun 2017 00:56:56: 12000000 INFO @ Wed, 28 Jun 2017 00:56:57: 12000000 INFO @ Wed, 28 Jun 2017 00:56:59: 12000000 INFO @ Wed, 28 Jun 2017 00:57:01: 13000000 INFO @ Wed, 28 Jun 2017 00:57:03: 13000000 INFO @ Wed, 28 Jun 2017 00:57:05: 13000000 INFO @ Wed, 28 Jun 2017 00:57:06: 14000000 INFO @ Wed, 28 Jun 2017 00:57:08: 14000000 INFO @ Wed, 28 Jun 2017 00:57:10: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:57:10: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:57:10: #1 total tags in treatment: 7189029 INFO @ Wed, 28 Jun 2017 00:57:10: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:57:10: #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 00:57:10: #1 tags after filtering in treatment: 5556266 INFO @ Wed, 28 Jun 2017 00:57:10: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 28 Jun 2017 00:57:10: #1 finished! INFO @ Wed, 28 Jun 2017 00:57:10: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:57:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:57:11: #2 number of paired peaks: 5537 INFO @ Wed, 28 Jun 2017 00:57:11: start model_add_line... INFO @ Wed, 28 Jun 2017 00:57:11: start X-correlation... INFO @ Wed, 28 Jun 2017 00:57:11: end of X-cor INFO @ Wed, 28 Jun 2017 00:57:11: #2 finished! INFO @ Wed, 28 Jun 2017 00:57:11: #2 predicted fragment length is 156 bps INFO @ Wed, 28 Jun 2017 00:57:11: #2 alternative fragment length(s) may be 156 bps INFO @ Wed, 28 Jun 2017 00:57:11: #2.2 Generate R script for model : SRX749070.05_model.r INFO @ Wed, 28 Jun 2017 00:57:11: 14000000 INFO @ Wed, 28 Jun 2017 00:57:11: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:57:11: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:57:12: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:57:12: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:57:12: #1 total tags in treatment: 7189029 INFO @ Wed, 28 Jun 2017 00:57:12: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:57:12: #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 00:57:12: #1 tags after filtering in treatment: 5556266 INFO @ Wed, 28 Jun 2017 00:57:12: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 28 Jun 2017 00:57:12: #1 finished! INFO @ Wed, 28 Jun 2017 00:57:12: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:57:12: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:57:13: #2 number of paired peaks: 5537 INFO @ Wed, 28 Jun 2017 00:57:13: start model_add_line... INFO @ Wed, 28 Jun 2017 00:57:13: start X-correlation... INFO @ Wed, 28 Jun 2017 00:57:13: end of X-cor INFO @ Wed, 28 Jun 2017 00:57:13: #2 finished! INFO @ Wed, 28 Jun 2017 00:57:13: #2 predicted fragment length is 156 bps INFO @ Wed, 28 Jun 2017 00:57:13: #2 alternative fragment length(s) may be 156 bps INFO @ Wed, 28 Jun 2017 00:57:13: #2.2 Generate R script for model : SRX749070.10_model.r INFO @ Wed, 28 Jun 2017 00:57:13: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:57:13: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:57:14: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:57:14: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:57:14: #1 total tags in treatment: 7189029 INFO @ Wed, 28 Jun 2017 00:57:14: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:57:14: #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 00:57:14: #1 tags after filtering in treatment: 5556266 INFO @ Wed, 28 Jun 2017 00:57:14: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 28 Jun 2017 00:57:14: #1 finished! INFO @ Wed, 28 Jun 2017 00:57:14: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:57:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:57:15: #2 number of paired peaks: 5537 INFO @ Wed, 28 Jun 2017 00:57:15: start model_add_line... INFO @ Wed, 28 Jun 2017 00:57:15: start X-correlation... INFO @ Wed, 28 Jun 2017 00:57:15: end of X-cor INFO @ Wed, 28 Jun 2017 00:57:15: #2 finished! INFO @ Wed, 28 Jun 2017 00:57:15: #2 predicted fragment length is 156 bps INFO @ Wed, 28 Jun 2017 00:57:15: #2 alternative fragment length(s) may be 156 bps INFO @ Wed, 28 Jun 2017 00:57:15: #2.2 Generate R script for model : SRX749070.20_model.r INFO @ Wed, 28 Jun 2017 00:57:15: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:57:15: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:57:28: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:57:30: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:57:32: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:57:36: #4 Write output xls file... SRX749070.05_peaks.xls INFO @ Wed, 28 Jun 2017 00:57:36: #4 Write peak in narrowPeak format file... SRX749070.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:57:36: #4 Write summits bed file... SRX749070.05_summits.bed INFO @ Wed, 28 Jun 2017 00:57:36: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9034 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 00:57:38: #4 Write output xls file... SRX749070.10_peaks.xls INFO @ Wed, 28 Jun 2017 00:57:38: #4 Write peak in narrowPeak format file... SRX749070.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:57:38: #4 Write summits bed file... SRX749070.10_summits.bed INFO @ Wed, 28 Jun 2017 00:57:38: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7610 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 00:57:40: #4 Write output xls file... SRX749070.20_peaks.xls INFO @ Wed, 28 Jun 2017 00:57:40: #4 Write peak in narrowPeak format file... SRX749070.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:57:41: #4 Write summits bed file... SRX749070.20_summits.bed INFO @ Wed, 28 Jun 2017 00:57:41: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5896 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。