Job ID = 9160036 sra ファイルのダウンロード中... Completed: 48682K bytes transferred in 3 seconds (108968K 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 1664562 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2574974/SRR5270923.sra Written 1664562 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: 00:00:53 1664562 reads; of these: 1664562 (100.00%) were paired; of these: 307996 (18.50%) aligned concordantly 0 times 1110331 (66.70%) aligned concordantly exactly 1 time 246235 (14.79%) aligned concordantly >1 times ---- 307996 pairs aligned concordantly 0 times; of these: 23612 (7.67%) aligned discordantly 1 time ---- 284384 pairs aligned 0 times concordantly or discordantly; of these: 568768 mates make up the pairs; of these: 525707 (92.43%) aligned 0 times 24505 (4.31%) aligned exactly 1 time 18556 (3.26%) aligned >1 times 84.21% overall alignment rate Time searching: 00:00:53 Overall time: 00:00:53 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] 12104 / 1379784 = 0.0088 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 01:45:01: # Command line: callpeak -t SRX2574974.bam -f BAM -g 12100000 -n SRX2574974.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2574974.20 # format = BAM # ChIP-seq file = ['SRX2574974.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 01:45:01: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:45:01: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:45:01: # Command line: callpeak -t SRX2574974.bam -f BAM -g 12100000 -n SRX2574974.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2574974.10 # format = BAM # ChIP-seq file = ['SRX2574974.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 01:45:01: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:45:01: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:45:01: # Command line: callpeak -t SRX2574974.bam -f BAM -g 12100000 -n SRX2574974.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2574974.05 # format = BAM # ChIP-seq file = ['SRX2574974.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 01:45:01: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:45:01: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:45:06: 1000000 INFO @ Wed, 28 Jun 2017 01:45:07: 1000000 INFO @ Wed, 28 Jun 2017 01:45:07: 1000000 INFO @ Wed, 28 Jun 2017 01:45:11: 2000000 INFO @ Wed, 28 Jun 2017 01:45:14: 2000000 INFO @ Wed, 28 Jun 2017 01:45:14: 2000000 INFO @ Wed, 28 Jun 2017 01:45:15: #1 tag size is determined as 26 bps INFO @ Wed, 28 Jun 2017 01:45:15: #1 tag size = 26 INFO @ Wed, 28 Jun 2017 01:45:15: #1 total tags in treatment: 1344499 INFO @ Wed, 28 Jun 2017 01:45:15: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:45:15: #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 01:45:15: #1 tags after filtering in treatment: 1126680 INFO @ Wed, 28 Jun 2017 01:45:15: #1 Redundant rate of treatment: 0.16 INFO @ Wed, 28 Jun 2017 01:45:15: #1 finished! INFO @ Wed, 28 Jun 2017 01:45:15: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:45:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:45:15: #2 number of paired peaks: 248 WARNING @ Wed, 28 Jun 2017 01:45:15: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Wed, 28 Jun 2017 01:45:15: start model_add_line... INFO @ Wed, 28 Jun 2017 01:45:15: start X-correlation... INFO @ Wed, 28 Jun 2017 01:45:15: end of X-cor INFO @ Wed, 28 Jun 2017 01:45:15: #2 finished! INFO @ Wed, 28 Jun 2017 01:45:15: #2 predicted fragment length is 184 bps INFO @ Wed, 28 Jun 2017 01:45:15: #2 alternative fragment length(s) may be 184 bps INFO @ Wed, 28 Jun 2017 01:45:15: #2.2 Generate R script for model : SRX2574974.20_model.r INFO @ Wed, 28 Jun 2017 01:45:15: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:45:15: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:45:19: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:45:19: #1 tag size is determined as 26 bps INFO @ Wed, 28 Jun 2017 01:45:19: #1 tag size = 26 INFO @ Wed, 28 Jun 2017 01:45:19: #1 total tags in treatment: 1344499 INFO @ Wed, 28 Jun 2017 01:45:19: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:45:19: #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 01:45:19: #1 tags after filtering in treatment: 1126680 INFO @ Wed, 28 Jun 2017 01:45:19: #1 Redundant rate of treatment: 0.16 INFO @ Wed, 28 Jun 2017 01:45:19: #1 finished! INFO @ Wed, 28 Jun 2017 01:45:19: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:45:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:45:19: #1 tag size is determined as 26 bps INFO @ Wed, 28 Jun 2017 01:45:19: #1 tag size = 26 INFO @ Wed, 28 Jun 2017 01:45:19: #1 total tags in treatment: 1344499 INFO @ Wed, 28 Jun 2017 01:45:19: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:45:19: #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 01:45:19: #1 tags after filtering in treatment: 1126680 INFO @ Wed, 28 Jun 2017 01:45:19: #1 Redundant rate of treatment: 0.16 INFO @ Wed, 28 Jun 2017 01:45:19: #1 finished! INFO @ Wed, 28 Jun 2017 01:45:19: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:45:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:45:19: #2 number of paired peaks: 248 WARNING @ Wed, 28 Jun 2017 01:45:19: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Wed, 28 Jun 2017 01:45:19: start model_add_line... INFO @ Wed, 28 Jun 2017 01:45:19: start X-correlation... INFO @ Wed, 28 Jun 2017 01:45:19: end of X-cor INFO @ Wed, 28 Jun 2017 01:45:19: #2 finished! INFO @ Wed, 28 Jun 2017 01:45:19: #2 predicted fragment length is 184 bps INFO @ Wed, 28 Jun 2017 01:45:19: #2 alternative fragment length(s) may be 184 bps INFO @ Wed, 28 Jun 2017 01:45:19: #2.2 Generate R script for model : SRX2574974.10_model.r INFO @ Wed, 28 Jun 2017 01:45:19: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:45:19: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:45:19: #2 number of paired peaks: 248 WARNING @ Wed, 28 Jun 2017 01:45:19: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Wed, 28 Jun 2017 01:45:19: start model_add_line... INFO @ Wed, 28 Jun 2017 01:45:19: start X-correlation... INFO @ Wed, 28 Jun 2017 01:45:19: end of X-cor INFO @ Wed, 28 Jun 2017 01:45:19: #2 finished! INFO @ Wed, 28 Jun 2017 01:45:19: #2 predicted fragment length is 184 bps INFO @ Wed, 28 Jun 2017 01:45:19: #2 alternative fragment length(s) may be 184 bps INFO @ Wed, 28 Jun 2017 01:45:19: #2.2 Generate R script for model : SRX2574974.05_model.r INFO @ Wed, 28 Jun 2017 01:45:19: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:45:19: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:45:20: #4 Write output xls file... SRX2574974.20_peaks.xls INFO @ Wed, 28 Jun 2017 01:45:20: #4 Write peak in narrowPeak format file... SRX2574974.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:45:20: #4 Write summits bed file... SRX2574974.20_summits.bed INFO @ Wed, 28 Jun 2017 01:45:20: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (342 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 01:45:23: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:45:23: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:45:25: #4 Write output xls file... SRX2574974.05_peaks.xls INFO @ Wed, 28 Jun 2017 01:45:25: #4 Write peak in narrowPeak format file... SRX2574974.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:45:25: #4 Write summits bed file... SRX2574974.05_summits.bed INFO @ Wed, 28 Jun 2017 01:45:25: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (868 records, 4 fields): 3 millis INFO @ Wed, 28 Jun 2017 01:45:25: #4 Write output xls file... SRX2574974.10_peaks.xls CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 01:45:25: #4 Write peak in narrowPeak format file... SRX2574974.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:45:25: #4 Write summits bed file... SRX2574974.10_summits.bed INFO @ Wed, 28 Jun 2017 01:45:25: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (572 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。