Job ID = 9159856 sra ファイルのダウンロード中... Completed: 393673K bytes transferred in 7 seconds (447957K 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 6065098 spots for /home/okishinya/chipatlas/results/dm3/SRX749051/SRR1636779.sra Written 6065098 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:23 6065098 reads; of these: 6065098 (100.00%) were paired; of these: 590796 (9.74%) aligned concordantly 0 times 4665529 (76.92%) aligned concordantly exactly 1 time 808773 (13.33%) aligned concordantly >1 times ---- 590796 pairs aligned concordantly 0 times; of these: 248266 (42.02%) aligned discordantly 1 time ---- 342530 pairs aligned 0 times concordantly or discordantly; of these: 685060 mates make up the pairs; of these: 358149 (52.28%) aligned 0 times 192674 (28.13%) aligned exactly 1 time 134237 (19.59%) aligned >1 times 97.05% overall alignment rate Time searching: 00:10:24 Overall time: 00:10:24 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] 39081 / 5719238 = 0.0068 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 00:33:03: # Command line: callpeak -t SRX749051.bam -f BAM -g dm -n SRX749051.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX749051.10 # format = BAM # ChIP-seq file = ['SRX749051.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 00:33:03: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:33:03: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:33:03: # Command line: callpeak -t SRX749051.bam -f BAM -g dm -n SRX749051.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX749051.05 # format = BAM # ChIP-seq file = ['SRX749051.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 00:33:03: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:33:03: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:33:03: # Command line: callpeak -t SRX749051.bam -f BAM -g dm -n SRX749051.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX749051.20 # format = BAM # ChIP-seq file = ['SRX749051.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 00:33:03: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:33:03: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:33:10: 1000000 INFO @ Wed, 28 Jun 2017 00:33:11: 1000000 INFO @ Wed, 28 Jun 2017 00:33:11: 1000000 INFO @ Wed, 28 Jun 2017 00:33:17: 2000000 INFO @ Wed, 28 Jun 2017 00:33:19: 2000000 INFO @ Wed, 28 Jun 2017 00:33:19: 2000000 INFO @ Wed, 28 Jun 2017 00:33:23: 3000000 INFO @ Wed, 28 Jun 2017 00:33:27: 3000000 INFO @ Wed, 28 Jun 2017 00:33:27: 3000000 INFO @ Wed, 28 Jun 2017 00:33:30: 4000000 INFO @ Wed, 28 Jun 2017 00:33:35: 4000000 INFO @ Wed, 28 Jun 2017 00:33:35: 4000000 INFO @ Wed, 28 Jun 2017 00:33:36: 5000000 INFO @ Wed, 28 Jun 2017 00:33:43: 6000000 INFO @ Wed, 28 Jun 2017 00:33:44: 5000000 INFO @ Wed, 28 Jun 2017 00:33:44: 5000000 INFO @ Wed, 28 Jun 2017 00:33:49: 7000000 INFO @ Wed, 28 Jun 2017 00:33:52: 6000000 INFO @ Wed, 28 Jun 2017 00:33:52: 6000000 INFO @ Wed, 28 Jun 2017 00:33:56: 8000000 INFO @ Wed, 28 Jun 2017 00:34:00: 7000000 INFO @ Wed, 28 Jun 2017 00:34:00: 7000000 INFO @ Wed, 28 Jun 2017 00:34:02: 9000000 INFO @ Wed, 28 Jun 2017 00:34:08: 8000000 INFO @ Wed, 28 Jun 2017 00:34:08: 8000000 INFO @ Wed, 28 Jun 2017 00:34:09: 10000000 INFO @ Wed, 28 Jun 2017 00:34:15: 11000000 INFO @ Wed, 28 Jun 2017 00:34:16: 9000000 INFO @ Wed, 28 Jun 2017 00:34:16: 9000000 INFO @ Wed, 28 Jun 2017 00:34:20: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:34:20: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:34:20: #1 total tags in treatment: 5435842 INFO @ Wed, 28 Jun 2017 00:34:20: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:34:20: #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 00:34:20: #1 tags after filtering in treatment: 5028576 INFO @ Wed, 28 Jun 2017 00:34:20: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 28 Jun 2017 00:34:20: #1 finished! INFO @ Wed, 28 Jun 2017 00:34:20: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:34:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:34:21: #2 number of paired peaks: 9407 INFO @ Wed, 28 Jun 2017 00:34:21: start model_add_line... INFO @ Wed, 28 Jun 2017 00:34:21: start X-correlation... INFO @ Wed, 28 Jun 2017 00:34:21: end of X-cor INFO @ Wed, 28 Jun 2017 00:34:21: #2 finished! INFO @ Wed, 28 Jun 2017 00:34:21: #2 predicted fragment length is 225 bps INFO @ Wed, 28 Jun 2017 00:34:21: #2 alternative fragment length(s) may be 225 bps INFO @ Wed, 28 Jun 2017 00:34:21: #2.2 Generate R script for model : SRX749051.10_model.r INFO @ Wed, 28 Jun 2017 00:34:21: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:34:21: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:34:24: 10000000 INFO @ Wed, 28 Jun 2017 00:34:24: 10000000 INFO @ Wed, 28 Jun 2017 00:34:32: 11000000 INFO @ Wed, 28 Jun 2017 00:34:32: 11000000 INFO @ Wed, 28 Jun 2017 00:34:35: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:34:37: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:34:37: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:34:37: #1 total tags in treatment: 5435842 INFO @ Wed, 28 Jun 2017 00:34:37: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:34:37: #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 00:34:37: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:34:37: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:34:37: #1 total tags in treatment: 5435842 INFO @ Wed, 28 Jun 2017 00:34:37: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:34:37: #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 00:34:37: #1 tags after filtering in treatment: 5028576 INFO @ Wed, 28 Jun 2017 00:34:37: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 28 Jun 2017 00:34:37: #1 finished! INFO @ Wed, 28 Jun 2017 00:34:37: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:34:37: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:34:37: #1 tags after filtering in treatment: 5028576 INFO @ Wed, 28 Jun 2017 00:34:37: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 28 Jun 2017 00:34:37: #1 finished! INFO @ Wed, 28 Jun 2017 00:34:37: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:34:37: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:34:38: #2 number of paired peaks: 9407 INFO @ Wed, 28 Jun 2017 00:34:38: start model_add_line... INFO @ Wed, 28 Jun 2017 00:34:38: #2 number of paired peaks: 9407 INFO @ Wed, 28 Jun 2017 00:34:38: start model_add_line... INFO @ Wed, 28 Jun 2017 00:34:38: start X-correlation... INFO @ Wed, 28 Jun 2017 00:34:38: start X-correlation... INFO @ Wed, 28 Jun 2017 00:34:38: end of X-cor INFO @ Wed, 28 Jun 2017 00:34:38: #2 finished! INFO @ Wed, 28 Jun 2017 00:34:38: #2 predicted fragment length is 225 bps INFO @ Wed, 28 Jun 2017 00:34:38: #2 alternative fragment length(s) may be 225 bps INFO @ Wed, 28 Jun 2017 00:34:38: #2.2 Generate R script for model : SRX749051.05_model.r INFO @ Wed, 28 Jun 2017 00:34:38: end of X-cor INFO @ Wed, 28 Jun 2017 00:34:38: #2 finished! INFO @ Wed, 28 Jun 2017 00:34:38: #2 predicted fragment length is 225 bps INFO @ Wed, 28 Jun 2017 00:34:38: #2 alternative fragment length(s) may be 225 bps INFO @ Wed, 28 Jun 2017 00:34:38: #2.2 Generate R script for model : SRX749051.20_model.r INFO @ Wed, 28 Jun 2017 00:34:38: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:34:38: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:34:38: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:34:38: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:34:42: #4 Write output xls file... SRX749051.10_peaks.xls INFO @ Wed, 28 Jun 2017 00:34:42: #4 Write peak in narrowPeak format file... SRX749051.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:34:43: #4 Write summits bed file... SRX749051.10_summits.bed INFO @ Wed, 28 Jun 2017 00:34:43: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6410 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 00:34:52: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:34:53: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:35:00: #4 Write output xls file... SRX749051.05_peaks.xls INFO @ Wed, 28 Jun 2017 00:35:00: #4 Write peak in narrowPeak format file... SRX749051.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:35:00: #4 Write summits bed file... SRX749051.05_summits.bed INFO @ Wed, 28 Jun 2017 00:35:00: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7560 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 00:35:01: #4 Write output xls file... SRX749051.20_peaks.xls INFO @ Wed, 28 Jun 2017 00:35:01: #4 Write peak in narrowPeak format file... SRX749051.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:35:01: #4 Write summits bed file... SRX749051.20_summits.bed INFO @ Wed, 28 Jun 2017 00:35:01: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4681 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。