Job ID = 9159867 sra ファイルのダウンロード中... Completed: 530225K bytes transferred in 7 seconds (586968K 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 9682311 spots for /home/okishinya/chipatlas/results/dm3/SRX749073/SRR1636801.sra Written 9682311 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: 00:23:02 9682311 reads; of these: 9682311 (100.00%) were paired; of these: 759379 (7.84%) aligned concordantly 0 times 6785600 (70.08%) aligned concordantly exactly 1 time 2137332 (22.07%) aligned concordantly >1 times ---- 759379 pairs aligned concordantly 0 times; of these: 9289 (1.22%) aligned discordantly 1 time ---- 750090 pairs aligned 0 times concordantly or discordantly; of these: 1500180 mates make up the pairs; of these: 1246736 (83.11%) aligned 0 times 181087 (12.07%) aligned exactly 1 time 72357 (4.82%) aligned >1 times 93.56% overall alignment rate Time searching: 00:23:02 Overall time: 00:23:02 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] 1749860 / 8923124 = 0.1961 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 00:55:00: # Command line: callpeak -t SRX749073.bam -f BAM -g dm -n SRX749073.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX749073.20 # format = BAM # ChIP-seq file = ['SRX749073.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 00:55:00: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:55:00: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:55:00: # Command line: callpeak -t SRX749073.bam -f BAM -g dm -n SRX749073.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX749073.10 # format = BAM # ChIP-seq file = ['SRX749073.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 00:55:00: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:55:00: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:55:00: # Command line: callpeak -t SRX749073.bam -f BAM -g dm -n SRX749073.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX749073.05 # format = BAM # ChIP-seq file = ['SRX749073.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 00:55:00: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:55:00: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:55:05: 1000000 INFO @ Wed, 28 Jun 2017 00:55:05: 1000000 INFO @ Wed, 28 Jun 2017 00:55:05: 1000000 INFO @ Wed, 28 Jun 2017 00:55:10: 2000000 INFO @ Wed, 28 Jun 2017 00:55:11: 2000000 INFO @ Wed, 28 Jun 2017 00:55:11: 2000000 INFO @ Wed, 28 Jun 2017 00:55:16: 3000000 INFO @ Wed, 28 Jun 2017 00:55:17: 3000000 INFO @ Wed, 28 Jun 2017 00:55:17: 3000000 INFO @ Wed, 28 Jun 2017 00:55:21: 4000000 INFO @ Wed, 28 Jun 2017 00:55:23: 4000000 INFO @ Wed, 28 Jun 2017 00:55:23: 4000000 INFO @ Wed, 28 Jun 2017 00:55:27: 5000000 INFO @ Wed, 28 Jun 2017 00:55:28: 5000000 INFO @ Wed, 28 Jun 2017 00:55:29: 5000000 INFO @ Wed, 28 Jun 2017 00:55:32: 6000000 INFO @ Wed, 28 Jun 2017 00:55:34: 6000000 INFO @ Wed, 28 Jun 2017 00:55:34: 6000000 INFO @ Wed, 28 Jun 2017 00:55:37: 7000000 INFO @ Wed, 28 Jun 2017 00:55:40: 7000000 INFO @ Wed, 28 Jun 2017 00:55:41: 7000000 INFO @ Wed, 28 Jun 2017 00:55:43: 8000000 INFO @ Wed, 28 Jun 2017 00:55:46: 8000000 INFO @ Wed, 28 Jun 2017 00:55:47: 8000000 INFO @ Wed, 28 Jun 2017 00:55:48: 9000000 INFO @ Wed, 28 Jun 2017 00:55:52: 9000000 INFO @ Wed, 28 Jun 2017 00:55:53: 9000000 INFO @ Wed, 28 Jun 2017 00:55:53: 10000000 INFO @ Wed, 28 Jun 2017 00:55:59: 10000000 INFO @ Wed, 28 Jun 2017 00:55:59: 11000000 INFO @ Wed, 28 Jun 2017 00:55:59: 10000000 INFO @ Wed, 28 Jun 2017 00:56:04: 12000000 INFO @ Wed, 28 Jun 2017 00:56:05: 11000000 INFO @ Wed, 28 Jun 2017 00:56:05: 11000000 INFO @ Wed, 28 Jun 2017 00:56:09: 13000000 INFO @ Wed, 28 Jun 2017 00:56:11: 12000000 INFO @ Wed, 28 Jun 2017 00:56:11: 12000000 INFO @ Wed, 28 Jun 2017 00:56:14: 14000000 INFO @ Wed, 28 Jun 2017 00:56:17: 13000000 INFO @ Wed, 28 Jun 2017 00:56:18: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:56:18: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:56:18: #1 total tags in treatment: 7173919 INFO @ Wed, 28 Jun 2017 00:56:18: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:56:18: #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 00:56:18: 13000000 INFO @ Wed, 28 Jun 2017 00:56:18: #1 tags after filtering in treatment: 6585925 INFO @ Wed, 28 Jun 2017 00:56:18: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 28 Jun 2017 00:56:18: #1 finished! INFO @ Wed, 28 Jun 2017 00:56:18: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:56:18: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:56:19: #2 number of paired peaks: 2099 INFO @ Wed, 28 Jun 2017 00:56:19: start model_add_line... INFO @ Wed, 28 Jun 2017 00:56:19: start X-correlation... INFO @ Wed, 28 Jun 2017 00:56:19: end of X-cor INFO @ Wed, 28 Jun 2017 00:56:19: #2 finished! INFO @ Wed, 28 Jun 2017 00:56:19: #2 predicted fragment length is 157 bps INFO @ Wed, 28 Jun 2017 00:56:19: #2 alternative fragment length(s) may be 157 bps INFO @ Wed, 28 Jun 2017 00:56:19: #2.2 Generate R script for model : SRX749073.05_model.r INFO @ Wed, 28 Jun 2017 00:56:19: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:56:19: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:56:23: 14000000 INFO @ Wed, 28 Jun 2017 00:56:24: 14000000 INFO @ Wed, 28 Jun 2017 00:56:27: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:56:27: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:56:27: #1 total tags in treatment: 7173919 INFO @ Wed, 28 Jun 2017 00:56:27: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:56:27: #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 00:56:27: #1 tags after filtering in treatment: 6585925 INFO @ Wed, 28 Jun 2017 00:56:27: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 28 Jun 2017 00:56:27: #1 finished! INFO @ Wed, 28 Jun 2017 00:56:27: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:56:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:56:28: #2 number of paired peaks: 2099 INFO @ Wed, 28 Jun 2017 00:56:28: start model_add_line... INFO @ Wed, 28 Jun 2017 00:56:28: start X-correlation... INFO @ Wed, 28 Jun 2017 00:56:28: end of X-cor INFO @ Wed, 28 Jun 2017 00:56:28: #2 finished! INFO @ Wed, 28 Jun 2017 00:56:28: #2 predicted fragment length is 157 bps INFO @ Wed, 28 Jun 2017 00:56:28: #2 alternative fragment length(s) may be 157 bps INFO @ Wed, 28 Jun 2017 00:56:28: #2.2 Generate R script for model : SRX749073.20_model.r INFO @ Wed, 28 Jun 2017 00:56:28: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:56:28: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:56:28: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:56:28: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:56:28: #1 total tags in treatment: 7173919 INFO @ Wed, 28 Jun 2017 00:56:28: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:56:28: #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 00:56:28: #1 tags after filtering in treatment: 6585925 INFO @ Wed, 28 Jun 2017 00:56:28: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 28 Jun 2017 00:56:28: #1 finished! INFO @ Wed, 28 Jun 2017 00:56:28: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:56:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:56:29: #2 number of paired peaks: 2099 INFO @ Wed, 28 Jun 2017 00:56:29: start model_add_line... INFO @ Wed, 28 Jun 2017 00:56:29: start X-correlation... INFO @ Wed, 28 Jun 2017 00:56:29: end of X-cor INFO @ Wed, 28 Jun 2017 00:56:29: #2 finished! INFO @ Wed, 28 Jun 2017 00:56:29: #2 predicted fragment length is 157 bps INFO @ Wed, 28 Jun 2017 00:56:29: #2 alternative fragment length(s) may be 157 bps INFO @ Wed, 28 Jun 2017 00:56:29: #2.2 Generate R script for model : SRX749073.10_model.r INFO @ Wed, 28 Jun 2017 00:56:29: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:56:29: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:56:35: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:56:44: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:56:45: #4 Write output xls file... SRX749073.05_peaks.xls INFO @ Wed, 28 Jun 2017 00:56:45: #4 Write peak in narrowPeak format file... SRX749073.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:56:45: #4 Write summits bed file... SRX749073.05_summits.bed INFO @ Wed, 28 Jun 2017 00:56:45: Done! INFO @ Wed, 28 Jun 2017 00:56:45: #3 Call peaks for each chromosome... pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7665 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 00:56:53: #4 Write output xls file... SRX749073.20_peaks.xls INFO @ Wed, 28 Jun 2017 00:56:53: #4 Write peak in narrowPeak format file... SRX749073.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:56:53: #4 Write summits bed file... SRX749073.20_summits.bed INFO @ Wed, 28 Jun 2017 00:56:53: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3145 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 00:56:56: #4 Write output xls file... SRX749073.10_peaks.xls INFO @ Wed, 28 Jun 2017 00:56:56: #4 Write peak in narrowPeak format file... SRX749073.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:56:56: #4 Write summits bed file... SRX749073.10_summits.bed INFO @ Wed, 28 Jun 2017 00:56:56: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5232 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。