Job ID = 2008157 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 699,502 reads read : 1,399,004 reads written : 1,399,004 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR628968.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: 00:00:30 699502 reads; of these: 699502 (100.00%) were paired; of these: 11976 (1.71%) aligned concordantly 0 times 625102 (89.36%) aligned concordantly exactly 1 time 62424 (8.92%) aligned concordantly >1 times ---- 11976 pairs aligned concordantly 0 times; of these: 4582 (38.26%) aligned discordantly 1 time ---- 7394 pairs aligned 0 times concordantly or discordantly; of these: 14788 mates make up the pairs; of these: 9681 (65.47%) aligned 0 times 2922 (19.76%) aligned exactly 1 time 2185 (14.78%) aligned >1 times 99.31% overall alignment rate Time searching: 00:00:30 Overall time: 00:00:30 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] 623052 / 691010 = 0.9017 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 17:31:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585698/ERX585698.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585698/ERX585698.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585698/ERX585698.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585698/ERX585698.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 17:31:08: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:31:08: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:31:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585698/ERX585698.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585698/ERX585698.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585698/ERX585698.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585698/ERX585698.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 17:31:09: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:31:09: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:31:09: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 17:31:09: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 17:31:09: #1 total tags in treatment: 68013 INFO @ Fri, 05 Jul 2019 17:31:09: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:31:09: #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 17:31:09: #1 tags after filtering in treatment: 65394 INFO @ Fri, 05 Jul 2019 17:31:09: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 05 Jul 2019 17:31:09: #1 finished! INFO @ Fri, 05 Jul 2019 17:31:09: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:31:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:31:09: #2 number of paired peaks: 179 WARNING @ Fri, 05 Jul 2019 17:31:09: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Fri, 05 Jul 2019 17:31:09: start model_add_line... INFO @ Fri, 05 Jul 2019 17:31:09: start X-correlation... INFO @ Fri, 05 Jul 2019 17:31:09: end of X-cor INFO @ Fri, 05 Jul 2019 17:31:09: #2 finished! INFO @ Fri, 05 Jul 2019 17:31:09: #2 predicted fragment length is 173 bps INFO @ Fri, 05 Jul 2019 17:31:09: #2 alternative fragment length(s) may be 18,41,65,102,173,196,212,240,304,324,404,424,454,475,518,551,577 bps INFO @ Fri, 05 Jul 2019 17:31:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585698/ERX585698.05_model.r INFO @ Fri, 05 Jul 2019 17:31:09: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:31:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:31:09: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:31:09: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585698/ERX585698.05_peaks.xls INFO @ Fri, 05 Jul 2019 17:31:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585698/ERX585698.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:31:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585698/ERX585698.05_summits.bed INFO @ Fri, 05 Jul 2019 17:31:09: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:31:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585698/ERX585698.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585698/ERX585698.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585698/ERX585698.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585698/ERX585698.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 17:31:10: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:31:10: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:31:10: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 17:31:10: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 17:31:10: #1 total tags in treatment: 68013 INFO @ Fri, 05 Jul 2019 17:31:10: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:31:10: #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 17:31:10: #1 tags after filtering in treatment: 65394 INFO @ Fri, 05 Jul 2019 17:31:10: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 05 Jul 2019 17:31:10: #1 finished! INFO @ Fri, 05 Jul 2019 17:31:10: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:31:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:31:10: #2 number of paired peaks: 179 WARNING @ Fri, 05 Jul 2019 17:31:10: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Fri, 05 Jul 2019 17:31:10: start model_add_line... INFO @ Fri, 05 Jul 2019 17:31:10: start X-correlation... INFO @ Fri, 05 Jul 2019 17:31:10: end of X-cor INFO @ Fri, 05 Jul 2019 17:31:10: #2 finished! INFO @ Fri, 05 Jul 2019 17:31:10: #2 predicted fragment length is 173 bps INFO @ Fri, 05 Jul 2019 17:31:10: #2 alternative fragment length(s) may be 18,41,65,102,173,196,212,240,304,324,404,424,454,475,518,551,577 bps INFO @ Fri, 05 Jul 2019 17:31:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585698/ERX585698.10_model.r INFO @ Fri, 05 Jul 2019 17:31:10: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:31:10: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 17:31:10: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:31:10: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585698/ERX585698.10_peaks.xls INFO @ Fri, 05 Jul 2019 17:31:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585698/ERX585698.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:31:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585698/ERX585698.10_summits.bed INFO @ Fri, 05 Jul 2019 17:31:10: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 17:31:11: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 17:31:11: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 17:31:11: #1 total tags in treatment: 68013 INFO @ Fri, 05 Jul 2019 17:31:11: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:31:11: #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 17:31:11: #1 tags after filtering in treatment: 65394 INFO @ Fri, 05 Jul 2019 17:31:11: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 05 Jul 2019 17:31:11: #1 finished! INFO @ Fri, 05 Jul 2019 17:31:11: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:31:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:31:11: #2 number of paired peaks: 179 WARNING @ Fri, 05 Jul 2019 17:31:11: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Fri, 05 Jul 2019 17:31:11: start model_add_line... INFO @ Fri, 05 Jul 2019 17:31:11: start X-correlation... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:31:11: end of X-cor INFO @ Fri, 05 Jul 2019 17:31:11: #2 finished! INFO @ Fri, 05 Jul 2019 17:31:11: #2 predicted fragment length is 173 bps INFO @ Fri, 05 Jul 2019 17:31:11: #2 alternative fragment length(s) may be 18,41,65,102,173,196,212,240,304,324,404,424,454,475,518,551,577 bps INFO @ Fri, 05 Jul 2019 17:31:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585698/ERX585698.20_model.r INFO @ Fri, 05 Jul 2019 17:31:11: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:31:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:31:11: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:31:11: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585698/ERX585698.20_peaks.xls INFO @ Fri, 05 Jul 2019 17:31:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585698/ERX585698.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:31:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585698/ERX585698.20_summits.bed INFO @ Fri, 05 Jul 2019 17:31:11: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling