Job ID = 2007716 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 22,388 reads read : 44,776 reads written : 44,776 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: 00:00:01 22388 reads; of these: 22388 (100.00%) were paired; of these: 1974 (8.82%) aligned concordantly 0 times 18846 (84.18%) aligned concordantly exactly 1 time 1568 (7.00%) aligned concordantly >1 times ---- 1974 pairs aligned concordantly 0 times; of these: 964 (48.83%) aligned discordantly 1 time ---- 1010 pairs aligned 0 times concordantly or discordantly; of these: 2020 mates make up the pairs; of these: 1393 (68.96%) aligned 0 times 407 (20.15%) aligned exactly 1 time 220 (10.89%) aligned >1 times 96.89% overall alignment rate Time searching: 00:00:01 Overall time: 00:00:01 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] 34 / 21158 = 0.0016 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 16:22:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX433670/ERX433670.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX433670/ERX433670.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX433670/ERX433670.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX433670/ERX433670.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 16:22:23: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:22:23: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:22:23: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:22:23: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:22:23: #1 total tags in treatment: 20381 INFO @ Fri, 05 Jul 2019 16:22:23: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:22:23: #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 16:22:23: #1 tags after filtering in treatment: 20341 INFO @ Fri, 05 Jul 2019 16:22:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:22:23: #1 finished! INFO @ Fri, 05 Jul 2019 16:22:23: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:22:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:22:23: #2 number of paired peaks: 239 WARNING @ Fri, 05 Jul 2019 16:22:23: Fewer paired peaks (239) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 239 pairs to build model! INFO @ Fri, 05 Jul 2019 16:22:23: start model_add_line... INFO @ Fri, 05 Jul 2019 16:22:23: start X-correlation... INFO @ Fri, 05 Jul 2019 16:22:23: end of X-cor INFO @ Fri, 05 Jul 2019 16:22:23: #2 finished! INFO @ Fri, 05 Jul 2019 16:22:23: #2 predicted fragment length is 264 bps INFO @ Fri, 05 Jul 2019 16:22:23: #2 alternative fragment length(s) may be 15,45,75,148,163,192,220,239,264,288,323,358,389,416,486,514,538,575 bps INFO @ Fri, 05 Jul 2019 16:22:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX433670/ERX433670.05_model.r INFO @ Fri, 05 Jul 2019 16:22:23: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:22:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:22:23: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:22:23: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX433670/ERX433670.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:22:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX433670/ERX433670.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:22:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX433670/ERX433670.05_summits.bed INFO @ Fri, 05 Jul 2019 16:22:23: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (2 records, 4 fields): 1 millis BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 16:22:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX433670/ERX433670.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX433670/ERX433670.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX433670/ERX433670.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX433670/ERX433670.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 16:22:24: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:22:24: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:22:24: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:22:24: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:22:24: #1 total tags in treatment: 20381 INFO @ Fri, 05 Jul 2019 16:22:24: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:22:24: #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 16:22:24: #1 tags after filtering in treatment: 20341 INFO @ Fri, 05 Jul 2019 16:22:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:22:24: #1 finished! INFO @ Fri, 05 Jul 2019 16:22:24: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:22:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:22:24: #2 number of paired peaks: 239 WARNING @ Fri, 05 Jul 2019 16:22:24: Fewer paired peaks (239) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 239 pairs to build model! INFO @ Fri, 05 Jul 2019 16:22:24: start model_add_line... INFO @ Fri, 05 Jul 2019 16:22:24: start X-correlation... INFO @ Fri, 05 Jul 2019 16:22:24: end of X-cor INFO @ Fri, 05 Jul 2019 16:22:24: #2 finished! INFO @ Fri, 05 Jul 2019 16:22:24: #2 predicted fragment length is 264 bps INFO @ Fri, 05 Jul 2019 16:22:24: #2 alternative fragment length(s) may be 15,45,75,148,163,192,220,239,264,288,323,358,389,416,486,514,538,575 bps INFO @ Fri, 05 Jul 2019 16:22:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX433670/ERX433670.10_model.r INFO @ Fri, 05 Jul 2019 16:22:24: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:22:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:22:24: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:22:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX433670/ERX433670.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:22:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX433670/ERX433670.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:22:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX433670/ERX433670.10_summits.bed INFO @ Fri, 05 Jul 2019 16:22:24: Done! pass1 - making usageList (0 chroms): 257 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) INFO @ Fri, 05 Jul 2019 16:22:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX433670/ERX433670.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX433670/ERX433670.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX433670/ERX433670.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX433670/ERX433670.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 16:22:25: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:22:25: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:22:25: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:22:25: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:22:25: #1 total tags in treatment: 20381 INFO @ Fri, 05 Jul 2019 16:22:25: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:22:25: #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 16:22:25: #1 tags after filtering in treatment: 20341 INFO @ Fri, 05 Jul 2019 16:22:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:22:25: #1 finished! INFO @ Fri, 05 Jul 2019 16:22:25: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:22:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:22:25: #2 number of paired peaks: 239 WARNING @ Fri, 05 Jul 2019 16:22:25: Fewer paired peaks (239) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 239 pairs to build model! INFO @ Fri, 05 Jul 2019 16:22:25: start model_add_line... INFO @ Fri, 05 Jul 2019 16:22:25: start X-correlation... INFO @ Fri, 05 Jul 2019 16:22:25: end of X-cor INFO @ Fri, 05 Jul 2019 16:22:25: #2 finished! INFO @ Fri, 05 Jul 2019 16:22:25: #2 predicted fragment length is 264 bps INFO @ Fri, 05 Jul 2019 16:22:25: #2 alternative fragment length(s) may be 15,45,75,148,163,192,220,239,264,288,323,358,389,416,486,514,538,575 bps INFO @ Fri, 05 Jul 2019 16:22:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX433670/ERX433670.20_model.r INFO @ Fri, 05 Jul 2019 16:22:25: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:22:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:22:25: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:22:25: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX433670/ERX433670.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:22:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX433670/ERX433670.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:22:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX433670/ERX433670.20_summits.bed INFO @ Fri, 05 Jul 2019 16:22:25: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling