Job ID = 9160037 sra ファイルのダウンロード中... Completed: 173726K bytes transferred in 5 seconds (262880K 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 7425319 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2574975/SRR5270924.sra Written 7425319 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: 00:02:24 7425319 reads; of these: 7425319 (100.00%) were paired; of these: 4633580 (62.40%) aligned concordantly 0 times 1950413 (26.27%) aligned concordantly exactly 1 time 841326 (11.33%) aligned concordantly >1 times ---- 4633580 pairs aligned concordantly 0 times; of these: 6392 (0.14%) aligned discordantly 1 time ---- 4627188 pairs aligned 0 times concordantly or discordantly; of these: 9254376 mates make up the pairs; of these: 6067757 (65.57%) aligned 0 times 2240858 (24.21%) aligned exactly 1 time 945761 (10.22%) aligned >1 times 59.14% overall alignment rate Time searching: 00:02:24 Overall time: 00:02:24 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 272074 / 2797275 = 0.0973 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 01:48:35: # Command line: callpeak -t SRX2574975.bam -f BAM -g 12100000 -n SRX2574975.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2574975.10 # format = BAM # ChIP-seq file = ['SRX2574975.bam'] # control file = None # effective genome size = 1.21e+07 # 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 01:48:35: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:48:35: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:48:35: # Command line: callpeak -t SRX2574975.bam -f BAM -g 12100000 -n SRX2574975.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2574975.05 # format = BAM # ChIP-seq file = ['SRX2574975.bam'] # control file = None # effective genome size = 1.21e+07 # 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 01:48:35: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:48:35: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:48:35: # Command line: callpeak -t SRX2574975.bam -f BAM -g 12100000 -n SRX2574975.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2574975.20 # format = BAM # ChIP-seq file = ['SRX2574975.bam'] # control file = None # effective genome size = 1.21e+07 # 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 01:48:35: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:48:35: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:48:40: 1000000 INFO @ Wed, 28 Jun 2017 01:48:40: 1000000 INFO @ Wed, 28 Jun 2017 01:48:40: 1000000 INFO @ Wed, 28 Jun 2017 01:48:44: 2000000 INFO @ Wed, 28 Jun 2017 01:48:44: 2000000 INFO @ Wed, 28 Jun 2017 01:48:45: 2000000 INFO @ Wed, 28 Jun 2017 01:48:49: 3000000 INFO @ Wed, 28 Jun 2017 01:48:49: 3000000 INFO @ Wed, 28 Jun 2017 01:48:49: 3000000 INFO @ Wed, 28 Jun 2017 01:48:54: 4000000 INFO @ Wed, 28 Jun 2017 01:48:54: 4000000 INFO @ Wed, 28 Jun 2017 01:48:54: 4000000 INFO @ Wed, 28 Jun 2017 01:48:58: 5000000 INFO @ Wed, 28 Jun 2017 01:48:58: 5000000 INFO @ Wed, 28 Jun 2017 01:48:59: 5000000 INFO @ Wed, 28 Jun 2017 01:49:03: 6000000 INFO @ Wed, 28 Jun 2017 01:49:03: 6000000 INFO @ Wed, 28 Jun 2017 01:49:04: 6000000 INFO @ Wed, 28 Jun 2017 01:49:07: 7000000 INFO @ Wed, 28 Jun 2017 01:49:07: 7000000 INFO @ Wed, 28 Jun 2017 01:49:09: 7000000 INFO @ Wed, 28 Jun 2017 01:49:12: 8000000 INFO @ Wed, 28 Jun 2017 01:49:12: 8000000 INFO @ Wed, 28 Jun 2017 01:49:13: #1 tag size is determined as 26 bps INFO @ Wed, 28 Jun 2017 01:49:13: #1 tag size = 26 INFO @ Wed, 28 Jun 2017 01:49:13: #1 total tags in treatment: 2519770 INFO @ Wed, 28 Jun 2017 01:49:13: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:49:13: #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 01:49:13: #1 tag size is determined as 26 bps INFO @ Wed, 28 Jun 2017 01:49:13: #1 tag size = 26 INFO @ Wed, 28 Jun 2017 01:49:13: #1 total tags in treatment: 2519770 INFO @ Wed, 28 Jun 2017 01:49:13: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:49:13: #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 01:49:13: #1 tags after filtering in treatment: 1719278 INFO @ Wed, 28 Jun 2017 01:49:13: #1 Redundant rate of treatment: 0.32 INFO @ Wed, 28 Jun 2017 01:49:13: #1 finished! INFO @ Wed, 28 Jun 2017 01:49:13: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:49:13: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:49:13: #1 tags after filtering in treatment: 1719278 INFO @ Wed, 28 Jun 2017 01:49:13: #1 Redundant rate of treatment: 0.32 INFO @ Wed, 28 Jun 2017 01:49:13: #1 finished! INFO @ Wed, 28 Jun 2017 01:49:13: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:49:13: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:49:13: #2 number of paired peaks: 117 WARNING @ Wed, 28 Jun 2017 01:49:13: Fewer paired peaks (117) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 117 pairs to build model! INFO @ Wed, 28 Jun 2017 01:49:13: start model_add_line... INFO @ Wed, 28 Jun 2017 01:49:14: start X-correlation... INFO @ Wed, 28 Jun 2017 01:49:14: end of X-cor INFO @ Wed, 28 Jun 2017 01:49:14: #2 finished! INFO @ Wed, 28 Jun 2017 01:49:14: #2 predicted fragment length is 163 bps INFO @ Wed, 28 Jun 2017 01:49:14: #2 alternative fragment length(s) may be 139,163,185 bps INFO @ Wed, 28 Jun 2017 01:49:14: #2.2 Generate R script for model : SRX2574975.20_model.r INFO @ Wed, 28 Jun 2017 01:49:14: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:49:14: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:49:14: #2 number of paired peaks: 117 WARNING @ Wed, 28 Jun 2017 01:49:14: Fewer paired peaks (117) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 117 pairs to build model! INFO @ Wed, 28 Jun 2017 01:49:14: start model_add_line... INFO @ Wed, 28 Jun 2017 01:49:14: start X-correlation... INFO @ Wed, 28 Jun 2017 01:49:14: end of X-cor INFO @ Wed, 28 Jun 2017 01:49:14: #2 finished! INFO @ Wed, 28 Jun 2017 01:49:14: #2 predicted fragment length is 163 bps INFO @ Wed, 28 Jun 2017 01:49:14: #2 alternative fragment length(s) may be 139,163,185 bps INFO @ Wed, 28 Jun 2017 01:49:14: #2.2 Generate R script for model : SRX2574975.10_model.r INFO @ Wed, 28 Jun 2017 01:49:14: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:49:14: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:49:14: 8000000 INFO @ Wed, 28 Jun 2017 01:49:15: #1 tag size is determined as 26 bps INFO @ Wed, 28 Jun 2017 01:49:15: #1 tag size = 26 INFO @ Wed, 28 Jun 2017 01:49:15: #1 total tags in treatment: 2519770 INFO @ Wed, 28 Jun 2017 01:49:15: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:49:15: #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 01:49:15: #1 tags after filtering in treatment: 1719278 INFO @ Wed, 28 Jun 2017 01:49:15: #1 Redundant rate of treatment: 0.32 INFO @ Wed, 28 Jun 2017 01:49:15: #1 finished! INFO @ Wed, 28 Jun 2017 01:49:15: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:49:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:49:15: #2 number of paired peaks: 117 WARNING @ Wed, 28 Jun 2017 01:49:15: Fewer paired peaks (117) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 117 pairs to build model! INFO @ Wed, 28 Jun 2017 01:49:15: start model_add_line... INFO @ Wed, 28 Jun 2017 01:49:15: start X-correlation... INFO @ Wed, 28 Jun 2017 01:49:15: end of X-cor INFO @ Wed, 28 Jun 2017 01:49:15: #2 finished! INFO @ Wed, 28 Jun 2017 01:49:15: #2 predicted fragment length is 163 bps INFO @ Wed, 28 Jun 2017 01:49:15: #2 alternative fragment length(s) may be 139,163,185 bps INFO @ Wed, 28 Jun 2017 01:49:15: #2.2 Generate R script for model : SRX2574975.05_model.r INFO @ Wed, 28 Jun 2017 01:49:15: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:49:15: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:49:19: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:49:19: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:49:20: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:49:20: #4 Write output xls file... SRX2574975.10_peaks.xls INFO @ Wed, 28 Jun 2017 01:49:20: #4 Write peak in narrowPeak format file... SRX2574975.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:49:20: #4 Write summits bed file... SRX2574975.10_summits.bed INFO @ Wed, 28 Jun 2017 01:49:20: Done! INFO @ Wed, 28 Jun 2017 01:49:21: #4 Write output xls file... SRX2574975.20_peaks.xls INFO @ Wed, 28 Jun 2017 01:49:21: #4 Write peak in narrowPeak format file... SRX2574975.20_peaks.narrowPeak pass1 - making usageList (16 chroms): 0 millis INFO @ Wed, 28 Jun 2017 01:49:21: #4 Write summits bed file... SRX2574975.20_summits.bed pass2 - checking and writing primary data (720 records, 4 fields): 4 millis INFO @ Wed, 28 Jun 2017 01:49:21: Done! CompletedMACS2peakCalling pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (361 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 01:49:22: #4 Write output xls file... SRX2574975.05_peaks.xls INFO @ Wed, 28 Jun 2017 01:49:22: #4 Write peak in narrowPeak format file... SRX2574975.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:49:22: #4 Write summits bed file... SRX2574975.05_summits.bed INFO @ Wed, 28 Jun 2017 01:49:22: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (1082 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。