Job ID = 2008183 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 66,991 reads read : 133,982 reads written : 133,982 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR628932.sra.cache’: 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: 00:00:03 66991 reads; of these: 66991 (100.00%) were paired; of these: 10287 (15.36%) aligned concordantly 0 times 51024 (76.17%) aligned concordantly exactly 1 time 5680 (8.48%) aligned concordantly >1 times ---- 10287 pairs aligned concordantly 0 times; of these: 1278 (12.42%) aligned discordantly 1 time ---- 9009 pairs aligned 0 times concordantly or discordantly; of these: 18018 mates make up the pairs; of these: 16669 (92.51%) aligned 0 times 371 (2.06%) aligned exactly 1 time 978 (5.43%) aligned >1 times 87.56% overall alignment rate Time searching: 00:00:03 Overall time: 00:00:03 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] 50415 / 57752 = 0.8730 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 17:33:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585718/ERX585718.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585718/ERX585718.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585718/ERX585718.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585718/ERX585718.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 17:33:35: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:33:35: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:33:35: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 17:33:35: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 17:33:35: #1 total tags in treatment: 7329 INFO @ Fri, 05 Jul 2019 17:33:35: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:33:35: #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 17:33:35: #1 tags after filtering in treatment: 7126 INFO @ Fri, 05 Jul 2019 17:33:35: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 05 Jul 2019 17:33:35: #1 finished! INFO @ Fri, 05 Jul 2019 17:33:35: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:33:35: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 17:33:35: #2 number of paired peaks: 341 WARNING @ Fri, 05 Jul 2019 17:33:35: Fewer paired peaks (341) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 341 pairs to build model! INFO @ Fri, 05 Jul 2019 17:33:35: start model_add_line... INFO @ Fri, 05 Jul 2019 17:33:35: start X-correlation... INFO @ Fri, 05 Jul 2019 17:33:35: end of X-cor INFO @ Fri, 05 Jul 2019 17:33:35: #2 finished! INFO @ Fri, 05 Jul 2019 17:33:35: #2 predicted fragment length is 294 bps INFO @ Fri, 05 Jul 2019 17:33:35: #2 alternative fragment length(s) may be 46,250,294,338,477 bps INFO @ Fri, 05 Jul 2019 17:33:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585718/ERX585718.05_model.r INFO @ Fri, 05 Jul 2019 17:33:35: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:33:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:33:35: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:33:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585718/ERX585718.05_peaks.xls INFO @ Fri, 05 Jul 2019 17:33:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585718/ERX585718.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:33:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585718/ERX585718.05_summits.bed INFO @ Fri, 05 Jul 2019 17:33:35: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:33:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585718/ERX585718.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585718/ERX585718.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585718/ERX585718.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585718/ERX585718.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 17:33:36: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:33:36: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:33:36: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 17:33:36: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 17:33:36: #1 total tags in treatment: 7329 INFO @ Fri, 05 Jul 2019 17:33:36: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:33:36: #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 17:33:36: #1 tags after filtering in treatment: 7126 INFO @ Fri, 05 Jul 2019 17:33:36: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 05 Jul 2019 17:33:36: #1 finished! INFO @ Fri, 05 Jul 2019 17:33:36: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:33:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:33:36: #2 number of paired peaks: 341 WARNING @ Fri, 05 Jul 2019 17:33:36: Fewer paired peaks (341) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 341 pairs to build model! INFO @ Fri, 05 Jul 2019 17:33:36: start model_add_line... INFO @ Fri, 05 Jul 2019 17:33:36: start X-correlation... INFO @ Fri, 05 Jul 2019 17:33:36: end of X-cor INFO @ Fri, 05 Jul 2019 17:33:36: #2 finished! INFO @ Fri, 05 Jul 2019 17:33:36: #2 predicted fragment length is 294 bps INFO @ Fri, 05 Jul 2019 17:33:36: #2 alternative fragment length(s) may be 46,250,294,338,477 bps INFO @ Fri, 05 Jul 2019 17:33:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585718/ERX585718.10_model.r INFO @ Fri, 05 Jul 2019 17:33:36: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:33:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:33:36: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:33:36: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585718/ERX585718.10_peaks.xls INFO @ Fri, 05 Jul 2019 17:33:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585718/ERX585718.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:33:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585718/ERX585718.10_summits.bed INFO @ Fri, 05 Jul 2019 17:33:36: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) INFO @ Fri, 05 Jul 2019 17:33:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585718/ERX585718.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585718/ERX585718.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585718/ERX585718.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585718/ERX585718.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 17:33:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:33:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:33:37: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 17:33:37: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 17:33:37: #1 total tags in treatment: 7329 INFO @ Fri, 05 Jul 2019 17:33:37: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:33:37: #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 17:33:37: #1 tags after filtering in treatment: 7126 INFO @ Fri, 05 Jul 2019 17:33:37: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 05 Jul 2019 17:33:37: #1 finished! INFO @ Fri, 05 Jul 2019 17:33:37: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:33:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:33:37: #2 number of paired peaks: 341 WARNING @ Fri, 05 Jul 2019 17:33:37: Fewer paired peaks (341) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 341 pairs to build model! INFO @ Fri, 05 Jul 2019 17:33:37: start model_add_line... INFO @ Fri, 05 Jul 2019 17:33:37: start X-correlation... INFO @ Fri, 05 Jul 2019 17:33:37: end of X-cor INFO @ Fri, 05 Jul 2019 17:33:37: #2 finished! INFO @ Fri, 05 Jul 2019 17:33:37: #2 predicted fragment length is 294 bps INFO @ Fri, 05 Jul 2019 17:33:37: #2 alternative fragment length(s) may be 46,250,294,338,477 bps INFO @ Fri, 05 Jul 2019 17:33:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585718/ERX585718.20_model.r INFO @ Fri, 05 Jul 2019 17:33:37: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:33:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:33:37: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:33:37: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585718/ERX585718.20_peaks.xls INFO @ Fri, 05 Jul 2019 17:33:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585718/ERX585718.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:33:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585718/ERX585718.20_summits.bed INFO @ Fri, 05 Jul 2019 17:33:37: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling CompletedMACS2peakCalling