Job ID = 10320359 sra ファイルのダウンロード中... Completed: 445841K bytes transferred in 58 seconds (61945K bits/sec), in 1 file. 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 19298405 spots for /home/okishinya/chipatlas/results/dm3/SRX3293411/SRR6183238.sra Written 19298405 spots total rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません 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: 01:01:05 19298405 reads; of these: 19298405 (100.00%) were paired; of these: 2555123 (13.24%) aligned concordantly 0 times 1565072 (8.11%) aligned concordantly exactly 1 time 15178210 (78.65%) aligned concordantly >1 times ---- 2555123 pairs aligned concordantly 0 times; of these: 59089 (2.31%) aligned discordantly 1 time ---- 2496034 pairs aligned 0 times concordantly or discordantly; of these: 4992068 mates make up the pairs; of these: 3592990 (71.97%) aligned 0 times 248892 (4.99%) aligned exactly 1 time 1150186 (23.04%) aligned >1 times 90.69% overall alignment rate Time searching: 01:01:05 Overall time: 01:01:05 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] 12138555 / 16629900 = 0.7299 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 @ Thu, 11 Jan 2018 03:14:39: # Command line: callpeak -t SRX3293411.bam -f BAM -g dm -n SRX3293411.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3293411.05 # format = BAM # ChIP-seq file = ['SRX3293411.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 @ Thu, 11 Jan 2018 03:14:39: # Command line: callpeak -t SRX3293411.bam -f BAM -g dm -n SRX3293411.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3293411.20 # format = BAM # ChIP-seq file = ['SRX3293411.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 @ Thu, 11 Jan 2018 03:14:39: # Command line: callpeak -t SRX3293411.bam -f BAM -g dm -n SRX3293411.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3293411.10 # format = BAM # ChIP-seq file = ['SRX3293411.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 @ Thu, 11 Jan 2018 03:14:39: #1 read tag files... INFO @ Thu, 11 Jan 2018 03:14:39: #1 read tag files... INFO @ Thu, 11 Jan 2018 03:14:39: #1 read tag files... INFO @ Thu, 11 Jan 2018 03:14:39: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 03:14:39: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 03:14:39: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 03:14:45: 1000000 INFO @ Thu, 11 Jan 2018 03:14:45: 1000000 INFO @ Thu, 11 Jan 2018 03:14:46: 1000000 INFO @ Thu, 11 Jan 2018 03:14:52: 2000000 INFO @ Thu, 11 Jan 2018 03:14:52: 2000000 INFO @ Thu, 11 Jan 2018 03:14:53: 2000000 INFO @ Thu, 11 Jan 2018 03:14:58: 3000000 INFO @ Thu, 11 Jan 2018 03:14:58: 3000000 INFO @ Thu, 11 Jan 2018 03:15:00: 3000000 INFO @ Thu, 11 Jan 2018 03:15:05: 4000000 INFO @ Thu, 11 Jan 2018 03:15:05: 4000000 INFO @ Thu, 11 Jan 2018 03:15:08: 4000000 INFO @ Thu, 11 Jan 2018 03:15:11: 5000000 INFO @ Thu, 11 Jan 2018 03:15:11: 5000000 INFO @ Thu, 11 Jan 2018 03:15:15: 5000000 INFO @ Thu, 11 Jan 2018 03:15:18: 6000000 INFO @ Thu, 11 Jan 2018 03:15:18: 6000000 INFO @ Thu, 11 Jan 2018 03:15:22: 6000000 INFO @ Thu, 11 Jan 2018 03:15:24: 7000000 INFO @ Thu, 11 Jan 2018 03:15:24: 7000000 INFO @ Thu, 11 Jan 2018 03:15:29: 7000000 INFO @ Thu, 11 Jan 2018 03:15:30: 8000000 INFO @ Thu, 11 Jan 2018 03:15:30: 8000000 INFO @ Thu, 11 Jan 2018 03:15:36: 9000000 INFO @ Thu, 11 Jan 2018 03:15:36: 9000000 INFO @ Thu, 11 Jan 2018 03:15:36: 8000000 INFO @ Thu, 11 Jan 2018 03:15:43: 10000000 INFO @ Thu, 11 Jan 2018 03:15:43: 10000000 INFO @ Thu, 11 Jan 2018 03:15:43: 9000000 INFO @ Thu, 11 Jan 2018 03:15:47: #1 tag size is determined as 25 bps INFO @ Thu, 11 Jan 2018 03:15:47: #1 tag size = 25 INFO @ Thu, 11 Jan 2018 03:15:47: #1 total tags in treatment: 4609577 INFO @ Thu, 11 Jan 2018 03:15:47: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 03:15:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 03:15:47: #1 tag size is determined as 25 bps INFO @ Thu, 11 Jan 2018 03:15:47: #1 tag size = 25 INFO @ Thu, 11 Jan 2018 03:15:47: #1 total tags in treatment: 4609577 INFO @ Thu, 11 Jan 2018 03:15:47: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 03:15:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 03:15:47: #1 tags after filtering in treatment: 2605839 INFO @ Thu, 11 Jan 2018 03:15:47: #1 Redundant rate of treatment: 0.43 INFO @ Thu, 11 Jan 2018 03:15:47: #1 finished! INFO @ Thu, 11 Jan 2018 03:15:47: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 03:15:47: #1 tags after filtering in treatment: 2605839 INFO @ Thu, 11 Jan 2018 03:15:47: #1 Redundant rate of treatment: 0.43 INFO @ Thu, 11 Jan 2018 03:15:47: #1 finished! INFO @ Thu, 11 Jan 2018 03:15:47: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 03:15:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 03:15:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 03:15:48: #2 number of paired peaks: 3435 INFO @ Thu, 11 Jan 2018 03:15:48: start model_add_line... INFO @ Thu, 11 Jan 2018 03:15:48: #2 number of paired peaks: 3435 INFO @ Thu, 11 Jan 2018 03:15:48: start model_add_line... INFO @ Thu, 11 Jan 2018 03:15:48: start X-correlation... INFO @ Thu, 11 Jan 2018 03:15:48: start X-correlation... INFO @ Thu, 11 Jan 2018 03:15:48: end of X-cor INFO @ Thu, 11 Jan 2018 03:15:48: end of X-cor INFO @ Thu, 11 Jan 2018 03:15:48: #2 finished! INFO @ Thu, 11 Jan 2018 03:15:48: #2 finished! INFO @ Thu, 11 Jan 2018 03:15:48: #2 predicted fragment length is 137 bps INFO @ Thu, 11 Jan 2018 03:15:48: #2 predicted fragment length is 137 bps INFO @ Thu, 11 Jan 2018 03:15:48: #2 alternative fragment length(s) may be 137 bps INFO @ Thu, 11 Jan 2018 03:15:48: #2 alternative fragment length(s) may be 137 bps INFO @ Thu, 11 Jan 2018 03:15:48: #2.2 Generate R script for model : SRX3293411.05_model.r INFO @ Thu, 11 Jan 2018 03:15:48: #2.2 Generate R script for model : SRX3293411.20_model.r INFO @ Thu, 11 Jan 2018 03:15:48: #3 Call peaks... INFO @ Thu, 11 Jan 2018 03:15:48: #3 Call peaks... INFO @ Thu, 11 Jan 2018 03:15:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 03:15:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 03:15:50: 10000000 INFO @ Thu, 11 Jan 2018 03:15:54: #1 tag size is determined as 25 bps INFO @ Thu, 11 Jan 2018 03:15:54: #1 tag size = 25 INFO @ Thu, 11 Jan 2018 03:15:54: #1 total tags in treatment: 4609577 INFO @ Thu, 11 Jan 2018 03:15:54: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 03:15:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 03:15:54: #1 tags after filtering in treatment: 2605839 INFO @ Thu, 11 Jan 2018 03:15:54: #1 Redundant rate of treatment: 0.43 INFO @ Thu, 11 Jan 2018 03:15:54: #1 finished! INFO @ Thu, 11 Jan 2018 03:15:54: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 03:15:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 03:15:54: #2 number of paired peaks: 3435 INFO @ Thu, 11 Jan 2018 03:15:54: start model_add_line... INFO @ Thu, 11 Jan 2018 03:15:54: start X-correlation... INFO @ Thu, 11 Jan 2018 03:15:54: end of X-cor INFO @ Thu, 11 Jan 2018 03:15:54: #2 finished! INFO @ Thu, 11 Jan 2018 03:15:54: #2 predicted fragment length is 137 bps INFO @ Thu, 11 Jan 2018 03:15:54: #2 alternative fragment length(s) may be 137 bps INFO @ Thu, 11 Jan 2018 03:15:54: #2.2 Generate R script for model : SRX3293411.10_model.r INFO @ Thu, 11 Jan 2018 03:15:54: #3 Call peaks... INFO @ Thu, 11 Jan 2018 03:15:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 03:15:55: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 03:15:56: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 03:15:59: #4 Write output xls file... SRX3293411.05_peaks.xls INFO @ Thu, 11 Jan 2018 03:15:59: #4 Write peak in narrowPeak format file... SRX3293411.05_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 03:15:59: #4 Write summits bed file... SRX3293411.05_summits.bed INFO @ Thu, 11 Jan 2018 03:15:59: Done! INFO @ Thu, 11 Jan 2018 03:15:59: #4 Write output xls file... SRX3293411.20_peaks.xls INFO @ Thu, 11 Jan 2018 03:15:59: #4 Write peak in narrowPeak format file... SRX3293411.20_peaks.narrowPeak pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2994 records, 4 fields): 7 millis INFO @ Thu, 11 Jan 2018 03:15:59: #4 Write summits bed file... SRX3293411.20_summits.bed CompletedMACS2peakCalling INFO @ Thu, 11 Jan 2018 03:15:59: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (970 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 11 Jan 2018 03:16:02: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 03:16:06: #4 Write output xls file... SRX3293411.10_peaks.xls INFO @ Thu, 11 Jan 2018 03:16:06: #4 Write peak in narrowPeak format file... SRX3293411.10_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 03:16:06: #4 Write summits bed file... SRX3293411.10_summits.bed INFO @ Thu, 11 Jan 2018 03:16:06: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1764 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。