Job ID = 2008200 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,577,043 reads read : 11,154,086 reads written : 11,154,086 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:04:52 5577043 reads; of these: 5577043 (100.00%) were paired; of these: 419742 (7.53%) aligned concordantly 0 times 4642712 (83.25%) aligned concordantly exactly 1 time 514589 (9.23%) aligned concordantly >1 times ---- 419742 pairs aligned concordantly 0 times; of these: 25200 (6.00%) aligned discordantly 1 time ---- 394542 pairs aligned 0 times concordantly or discordantly; of these: 789084 mates make up the pairs; of these: 754073 (95.56%) aligned 0 times 19024 (2.41%) aligned exactly 1 time 15987 (2.03%) aligned >1 times 93.24% overall alignment rate Time searching: 00:04:52 Overall time: 00:04:52 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] 4956873 / 5177490 = 0.9574 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 @ Fri, 05 Jul 2019 17:53:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585735/ERX585735.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585735/ERX585735.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585735/ERX585735.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585735/ERX585735.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 @ Fri, 05 Jul 2019 17:53:12: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:53:12: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:53:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585735/ERX585735.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585735/ERX585735.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585735/ERX585735.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585735/ERX585735.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 @ Fri, 05 Jul 2019 17:53:13: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:53:13: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:53:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585735/ERX585735.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585735/ERX585735.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585735/ERX585735.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585735/ERX585735.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 @ Fri, 05 Jul 2019 17:53:14: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:53:14: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:53:15: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 17:53:15: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 17:53:15: #1 total tags in treatment: 220426 INFO @ Fri, 05 Jul 2019 17:53:15: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:53:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 17:53:15: #1 tags after filtering in treatment: 192924 INFO @ Fri, 05 Jul 2019 17:53:15: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 05 Jul 2019 17:53:15: #1 finished! INFO @ Fri, 05 Jul 2019 17:53:15: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:53:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:53:15: #2 number of paired peaks: 426 WARNING @ Fri, 05 Jul 2019 17:53:15: Fewer paired peaks (426) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 426 pairs to build model! INFO @ Fri, 05 Jul 2019 17:53:15: start model_add_line... INFO @ Fri, 05 Jul 2019 17:53:15: start X-correlation... INFO @ Fri, 05 Jul 2019 17:53:15: end of X-cor INFO @ Fri, 05 Jul 2019 17:53:15: #2 finished! INFO @ Fri, 05 Jul 2019 17:53:15: #2 predicted fragment length is 156 bps INFO @ Fri, 05 Jul 2019 17:53:15: #2 alternative fragment length(s) may be 23,45,156,181,220,259,308,320,469,538,580 bps INFO @ Fri, 05 Jul 2019 17:53:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585735/ERX585735.05_model.r INFO @ Fri, 05 Jul 2019 17:53:15: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:53:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:53:16: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 17:53:16: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 17:53:16: #1 total tags in treatment: 220426 INFO @ Fri, 05 Jul 2019 17:53:16: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:53:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 17:53:16: #1 tags after filtering in treatment: 192924 INFO @ Fri, 05 Jul 2019 17:53:16: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 05 Jul 2019 17:53:16: #1 finished! INFO @ Fri, 05 Jul 2019 17:53:16: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:53:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:53:16: #2 number of paired peaks: 426 WARNING @ Fri, 05 Jul 2019 17:53:16: Fewer paired peaks (426) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 426 pairs to build model! INFO @ Fri, 05 Jul 2019 17:53:16: start model_add_line... INFO @ Fri, 05 Jul 2019 17:53:16: start X-correlation... INFO @ Fri, 05 Jul 2019 17:53:16: end of X-cor INFO @ Fri, 05 Jul 2019 17:53:16: #2 finished! INFO @ Fri, 05 Jul 2019 17:53:16: #2 predicted fragment length is 156 bps INFO @ Fri, 05 Jul 2019 17:53:16: #2 alternative fragment length(s) may be 23,45,156,181,220,259,308,320,469,538,580 bps INFO @ Fri, 05 Jul 2019 17:53:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585735/ERX585735.10_model.r INFO @ Fri, 05 Jul 2019 17:53:16: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:53:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:53:16: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:53:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585735/ERX585735.05_peaks.xls INFO @ Fri, 05 Jul 2019 17:53:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585735/ERX585735.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:53:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585735/ERX585735.05_summits.bed INFO @ Fri, 05 Jul 2019 17:53:16: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (85 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 17:53:17: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:53:17: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585735/ERX585735.10_peaks.xls INFO @ Fri, 05 Jul 2019 17:53:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585735/ERX585735.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:53:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585735/ERX585735.10_summits.bed INFO @ Fri, 05 Jul 2019 17:53:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (9 records, 4 fields): 1 millis INFO @ Fri, 05 Jul 2019 17:53:17: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 17:53:17: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 17:53:17: #1 total tags in treatment: 220426 INFO @ Fri, 05 Jul 2019 17:53:17: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:53:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 17:53:17: #1 tags after filtering in treatment: 192924 INFO @ Fri, 05 Jul 2019 17:53:17: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 05 Jul 2019 17:53:17: #1 finished! INFO @ Fri, 05 Jul 2019 17:53:17: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:53:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:53:17: #2 number of paired peaks: 426 WARNING @ Fri, 05 Jul 2019 17:53:17: Fewer paired peaks (426) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 426 pairs to build model! INFO @ Fri, 05 Jul 2019 17:53:17: start model_add_line... INFO @ Fri, 05 Jul 2019 17:53:17: start X-correlation... INFO @ Fri, 05 Jul 2019 17:53:17: end of X-cor INFO @ Fri, 05 Jul 2019 17:53:17: #2 finished! INFO @ Fri, 05 Jul 2019 17:53:17: #2 predicted fragment length is 156 bps INFO @ Fri, 05 Jul 2019 17:53:17: #2 alternative fragment length(s) may be 23,45,156,181,220,259,308,320,469,538,580 bps INFO @ Fri, 05 Jul 2019 17:53:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585735/ERX585735.20_model.r INFO @ Fri, 05 Jul 2019 17:53:17: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:53:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:53:18: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:53:18: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585735/ERX585735.20_peaks.xls INFO @ Fri, 05 Jul 2019 17:53:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585735/ERX585735.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:53:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585735/ERX585735.20_summits.bed INFO @ Fri, 05 Jul 2019 17:53:18: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。