Job ID = 9730446 sra ファイルのダウンロード中... Completed: 1373025K bytes transferred in 26 seconds (430798K 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 19825079 spots for /home/okishinya/chipatlas/results/dm3/SRX2559033/SRR5253497.sra Written 19825079 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: 00:25:20 19825079 reads; of these: 19825079 (100.00%) were paired; of these: 2049997 (10.34%) aligned concordantly 0 times 15762375 (79.51%) aligned concordantly exactly 1 time 2012707 (10.15%) aligned concordantly >1 times ---- 2049997 pairs aligned concordantly 0 times; of these: 30854 (1.51%) aligned discordantly 1 time ---- 2019143 pairs aligned 0 times concordantly or discordantly; of these: 4038286 mates make up the pairs; of these: 2775039 (68.72%) aligned 0 times 951509 (23.56%) aligned exactly 1 time 311738 (7.72%) aligned >1 times 93.00% overall alignment rate Time searching: 00:25:20 Overall time: 00:25:20 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 16 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] 11492350 / 17784847 = 0.6462 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 @ Sun, 03 Sep 2017 01:30:05: # Command line: callpeak -t SRX2559033.bam -f BAM -g dm -n SRX2559033.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2559033.20 # format = BAM # ChIP-seq file = ['SRX2559033.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 @ Sun, 03 Sep 2017 01:30:05: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:30:05: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:30:05: # Command line: callpeak -t SRX2559033.bam -f BAM -g dm -n SRX2559033.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2559033.05 # format = BAM # ChIP-seq file = ['SRX2559033.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 @ Sun, 03 Sep 2017 01:30:05: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:30:05: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:30:05: # Command line: callpeak -t SRX2559033.bam -f BAM -g dm -n SRX2559033.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2559033.10 # format = BAM # ChIP-seq file = ['SRX2559033.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 @ Sun, 03 Sep 2017 01:30:05: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:30:05: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:30:11: 1000000 INFO @ Sun, 03 Sep 2017 01:30:11: 1000000 INFO @ Sun, 03 Sep 2017 01:30:11: 1000000 INFO @ Sun, 03 Sep 2017 01:30:16: 2000000 INFO @ Sun, 03 Sep 2017 01:30:16: 2000000 INFO @ Sun, 03 Sep 2017 01:30:17: 2000000 INFO @ Sun, 03 Sep 2017 01:30:22: 3000000 INFO @ Sun, 03 Sep 2017 01:30:22: 3000000 INFO @ Sun, 03 Sep 2017 01:30:23: 3000000 INFO @ Sun, 03 Sep 2017 01:30:28: 4000000 INFO @ Sun, 03 Sep 2017 01:30:28: 4000000 INFO @ Sun, 03 Sep 2017 01:30:28: 4000000 INFO @ Sun, 03 Sep 2017 01:30:33: 5000000 INFO @ Sun, 03 Sep 2017 01:30:34: 5000000 INFO @ Sun, 03 Sep 2017 01:30:34: 5000000 INFO @ Sun, 03 Sep 2017 01:30:39: 6000000 INFO @ Sun, 03 Sep 2017 01:30:40: 6000000 INFO @ Sun, 03 Sep 2017 01:30:40: 6000000 INFO @ Sun, 03 Sep 2017 01:30:45: 7000000 INFO @ Sun, 03 Sep 2017 01:30:46: 7000000 INFO @ Sun, 03 Sep 2017 01:30:46: 7000000 INFO @ Sun, 03 Sep 2017 01:30:50: 8000000 INFO @ Sun, 03 Sep 2017 01:30:51: 8000000 INFO @ Sun, 03 Sep 2017 01:30:52: 8000000 INFO @ Sun, 03 Sep 2017 01:30:56: 9000000 INFO @ Sun, 03 Sep 2017 01:30:57: 9000000 INFO @ Sun, 03 Sep 2017 01:30:57: 9000000 INFO @ Sun, 03 Sep 2017 01:31:02: 10000000 INFO @ Sun, 03 Sep 2017 01:31:03: 10000000 INFO @ Sun, 03 Sep 2017 01:31:03: 10000000 INFO @ Sun, 03 Sep 2017 01:31:08: 11000000 INFO @ Sun, 03 Sep 2017 01:31:09: 11000000 INFO @ Sun, 03 Sep 2017 01:31:09: 11000000 INFO @ Sun, 03 Sep 2017 01:31:13: 12000000 INFO @ Sun, 03 Sep 2017 01:31:15: 12000000 INFO @ Sun, 03 Sep 2017 01:31:15: 12000000 INFO @ Sun, 03 Sep 2017 01:31:19: 13000000 INFO @ Sun, 03 Sep 2017 01:31:21: 13000000 INFO @ Sun, 03 Sep 2017 01:31:21: 13000000 INFO @ Sun, 03 Sep 2017 01:31:25: #1 tag size is determined as 50 bps INFO @ Sun, 03 Sep 2017 01:31:25: #1 tag size = 50 INFO @ Sun, 03 Sep 2017 01:31:25: #1 total tags in treatment: 6287030 INFO @ Sun, 03 Sep 2017 01:31:25: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:31:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:31:25: #1 tags after filtering in treatment: 5956906 INFO @ Sun, 03 Sep 2017 01:31:25: #1 Redundant rate of treatment: 0.05 INFO @ Sun, 03 Sep 2017 01:31:25: #1 finished! INFO @ Sun, 03 Sep 2017 01:31:25: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:31:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:31:25: #2 number of paired peaks: 2190 INFO @ Sun, 03 Sep 2017 01:31:25: start model_add_line... INFO @ Sun, 03 Sep 2017 01:31:25: #1 tag size is determined as 50 bps INFO @ Sun, 03 Sep 2017 01:31:25: #1 tag size = 50 INFO @ Sun, 03 Sep 2017 01:31:25: #1 total tags in treatment: 6287030 INFO @ Sun, 03 Sep 2017 01:31:25: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:31:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:31:26: start X-correlation... INFO @ Sun, 03 Sep 2017 01:31:26: end of X-cor INFO @ Sun, 03 Sep 2017 01:31:26: #2 finished! INFO @ Sun, 03 Sep 2017 01:31:26: #2 predicted fragment length is 182 bps INFO @ Sun, 03 Sep 2017 01:31:26: #2 alternative fragment length(s) may be 182 bps INFO @ Sun, 03 Sep 2017 01:31:26: #2.2 Generate R script for model : SRX2559033.10_model.r INFO @ Sun, 03 Sep 2017 01:31:26: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:31:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:31:26: #1 tags after filtering in treatment: 5956906 INFO @ Sun, 03 Sep 2017 01:31:26: #1 Redundant rate of treatment: 0.05 INFO @ Sun, 03 Sep 2017 01:31:26: #1 finished! INFO @ Sun, 03 Sep 2017 01:31:26: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:31:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:31:26: #1 tag size is determined as 50 bps INFO @ Sun, 03 Sep 2017 01:31:26: #1 tag size = 50 INFO @ Sun, 03 Sep 2017 01:31:26: #1 total tags in treatment: 6287030 INFO @ Sun, 03 Sep 2017 01:31:26: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:31:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:31:26: #1 tags after filtering in treatment: 5956906 INFO @ Sun, 03 Sep 2017 01:31:26: #1 Redundant rate of treatment: 0.05 INFO @ Sun, 03 Sep 2017 01:31:26: #1 finished! INFO @ Sun, 03 Sep 2017 01:31:26: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:31:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:31:26: #2 number of paired peaks: 2190 INFO @ Sun, 03 Sep 2017 01:31:26: start model_add_line... INFO @ Sun, 03 Sep 2017 01:31:26: start X-correlation... INFO @ Sun, 03 Sep 2017 01:31:26: end of X-cor INFO @ Sun, 03 Sep 2017 01:31:26: #2 finished! INFO @ Sun, 03 Sep 2017 01:31:26: #2 predicted fragment length is 182 bps INFO @ Sun, 03 Sep 2017 01:31:26: #2 alternative fragment length(s) may be 182 bps INFO @ Sun, 03 Sep 2017 01:31:26: #2.2 Generate R script for model : SRX2559033.05_model.r INFO @ Sun, 03 Sep 2017 01:31:26: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:31:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:31:27: #2 number of paired peaks: 2190 INFO @ Sun, 03 Sep 2017 01:31:27: start model_add_line... INFO @ Sun, 03 Sep 2017 01:31:27: start X-correlation... INFO @ Sun, 03 Sep 2017 01:31:27: end of X-cor INFO @ Sun, 03 Sep 2017 01:31:27: #2 finished! INFO @ Sun, 03 Sep 2017 01:31:27: #2 predicted fragment length is 182 bps INFO @ Sun, 03 Sep 2017 01:31:27: #2 alternative fragment length(s) may be 182 bps INFO @ Sun, 03 Sep 2017 01:31:27: #2.2 Generate R script for model : SRX2559033.20_model.r INFO @ Sun, 03 Sep 2017 01:31:27: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:31:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:31:41: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:31:41: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:31:42: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:31:49: #4 Write output xls file... SRX2559033.10_peaks.xls INFO @ Sun, 03 Sep 2017 01:31:49: #4 Write peak in narrowPeak format file... SRX2559033.10_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:31:49: #4 Write summits bed file... SRX2559033.10_summits.bed INFO @ Sun, 03 Sep 2017 01:31:49: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3878 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:31:50: #4 Write output xls file... SRX2559033.20_peaks.xls INFO @ Sun, 03 Sep 2017 01:31:50: #4 Write peak in narrowPeak format file... SRX2559033.20_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:31:50: #4 Write summits bed file... SRX2559033.20_summits.bed INFO @ Sun, 03 Sep 2017 01:31:50: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1253 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:31:50: #4 Write output xls file... SRX2559033.05_peaks.xls INFO @ Sun, 03 Sep 2017 01:31:50: #4 Write peak in narrowPeak format file... SRX2559033.05_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:31:50: #4 Write summits bed file... SRX2559033.05_summits.bed INFO @ Sun, 03 Sep 2017 01:31:50: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (7062 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。