Job ID = 2008240 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 71,861 reads read : 143,722 reads written : 143,722 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR628929.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: 00:00:04 71861 reads; of these: 71861 (100.00%) were paired; of these: 4223 (5.88%) aligned concordantly 0 times 59381 (82.63%) aligned concordantly exactly 1 time 8257 (11.49%) aligned concordantly >1 times ---- 4223 pairs aligned concordantly 0 times; of these: 2111 (49.99%) aligned discordantly 1 time ---- 2112 pairs aligned 0 times concordantly or discordantly; of these: 4224 mates make up the pairs; of these: 2701 (63.94%) aligned 0 times 575 (13.61%) aligned exactly 1 time 948 (22.44%) aligned >1 times 98.12% overall alignment rate Time searching: 00:00:04 Overall time: 00:00:04 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] 62366 / 69170 = 0.9016 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 17:58:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585764/ERX585764.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585764/ERX585764.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585764/ERX585764.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585764/ERX585764.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 17:58:58: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:58:58: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:58:58: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 17:58:58: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 17:58:58: #1 total tags in treatment: 7138 INFO @ Fri, 05 Jul 2019 17:58:58: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:58:58: #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 17:58:58: #1 tags after filtering in treatment: 6644 INFO @ Fri, 05 Jul 2019 17:58:58: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 17:58:58: #1 finished! INFO @ Fri, 05 Jul 2019 17:58:58: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:58:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:58:58: #2 number of paired peaks: 300 WARNING @ Fri, 05 Jul 2019 17:58:58: Fewer paired peaks (300) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 300 pairs to build model! INFO @ Fri, 05 Jul 2019 17:58:58: start model_add_line... INFO @ Fri, 05 Jul 2019 17:58:58: start X-correlation... INFO @ Fri, 05 Jul 2019 17:58:58: end of X-cor INFO @ Fri, 05 Jul 2019 17:58:58: #2 finished! INFO @ Fri, 05 Jul 2019 17:58:58: #2 predicted fragment length is 296 bps INFO @ Fri, 05 Jul 2019 17:58:58: #2 alternative fragment length(s) may be 43,104,117,159,180,201,234,261,296,312,335,355,416,447,470,527 bps INFO @ Fri, 05 Jul 2019 17:58:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585764/ERX585764.05_model.r INFO @ Fri, 05 Jul 2019 17:58:58: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:58:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:58:58: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:58:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585764/ERX585764.05_peaks.xls INFO @ Fri, 05 Jul 2019 17:58:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585764/ERX585764.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:58:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585764/ERX585764.05_summits.bed INFO @ Fri, 05 Jul 2019 17:58:58: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:58:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585764/ERX585764.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585764/ERX585764.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585764/ERX585764.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585764/ERX585764.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 17:58:59: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:58:59: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:58:59: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 17:58:59: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 17:58:59: #1 total tags in treatment: 7138 INFO @ Fri, 05 Jul 2019 17:58:59: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:58:59: #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 17:58:59: #1 tags after filtering in treatment: 6644 INFO @ Fri, 05 Jul 2019 17:58:59: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 17:58:59: #1 finished! INFO @ Fri, 05 Jul 2019 17:58:59: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:58:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:58:59: #2 number of paired peaks: 300 WARNING @ Fri, 05 Jul 2019 17:58:59: Fewer paired peaks (300) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 300 pairs to build model! INFO @ Fri, 05 Jul 2019 17:58:59: start model_add_line... INFO @ Fri, 05 Jul 2019 17:58:59: start X-correlation... INFO @ Fri, 05 Jul 2019 17:58:59: end of X-cor INFO @ Fri, 05 Jul 2019 17:58:59: #2 finished! INFO @ Fri, 05 Jul 2019 17:58:59: #2 predicted fragment length is 296 bps INFO @ Fri, 05 Jul 2019 17:58:59: #2 alternative fragment length(s) may be 43,104,117,159,180,201,234,261,296,312,335,355,416,447,470,527 bps INFO @ Fri, 05 Jul 2019 17:58:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585764/ERX585764.10_model.r INFO @ Fri, 05 Jul 2019 17:58:59: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:58:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:58:59: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:58:59: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585764/ERX585764.10_peaks.xls INFO @ Fri, 05 Jul 2019 17:58:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585764/ERX585764.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:58:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585764/ERX585764.10_summits.bed INFO @ Fri, 05 Jul 2019 17:58:59: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 17:59:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585764/ERX585764.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585764/ERX585764.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585764/ERX585764.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585764/ERX585764.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 17:59:00: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:59:00: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:59:00: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 17:59:00: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 17:59:00: #1 total tags in treatment: 7138 INFO @ Fri, 05 Jul 2019 17:59:00: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:59:00: #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 17:59:00: #1 tags after filtering in treatment: 6644 INFO @ Fri, 05 Jul 2019 17:59:00: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 17:59:00: #1 finished! INFO @ Fri, 05 Jul 2019 17:59:00: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:59:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:59:00: #2 number of paired peaks: 300 WARNING @ Fri, 05 Jul 2019 17:59:00: Fewer paired peaks (300) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 300 pairs to build model! INFO @ Fri, 05 Jul 2019 17:59:00: start model_add_line... INFO @ Fri, 05 Jul 2019 17:59:00: start X-correlation... INFO @ Fri, 05 Jul 2019 17:59:00: end of X-cor INFO @ Fri, 05 Jul 2019 17:59:00: #2 finished! INFO @ Fri, 05 Jul 2019 17:59:00: #2 predicted fragment length is 296 bps INFO @ Fri, 05 Jul 2019 17:59:00: #2 alternative fragment length(s) may be 43,104,117,159,180,201,234,261,296,312,335,355,416,447,470,527 bps INFO @ Fri, 05 Jul 2019 17:59:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585764/ERX585764.20_model.r INFO @ Fri, 05 Jul 2019 17:59:00: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:59:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:59:00: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:59:00: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585764/ERX585764.20_peaks.xls INFO @ Fri, 05 Jul 2019 17:59:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585764/ERX585764.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:59:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585764/ERX585764.20_summits.bed INFO @ Fri, 05 Jul 2019 17:59:00: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling CompletedMACS2peakCalling