Job ID = 2008308 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 7,515,887 reads read : 15,031,774 reads written : 15,031,774 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR629043.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: 00:05:57 7515887 reads; of these: 7515887 (100.00%) were paired; of these: 445819 (5.93%) aligned concordantly 0 times 6505406 (86.56%) aligned concordantly exactly 1 time 564662 (7.51%) aligned concordantly >1 times ---- 445819 pairs aligned concordantly 0 times; of these: 122912 (27.57%) aligned discordantly 1 time ---- 322907 pairs aligned 0 times concordantly or discordantly; of these: 645814 mates make up the pairs; of these: 585488 (90.66%) aligned 0 times 31026 (4.80%) aligned exactly 1 time 29300 (4.54%) aligned >1 times 96.10% overall alignment rate Time searching: 00:05:57 Overall time: 00:05:57 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] 6737749 / 7187559 = 0.9374 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 18:37:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585818/ERX585818.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585818/ERX585818.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585818/ERX585818.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585818/ERX585818.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 18:37:29: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:37:29: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:37:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585818/ERX585818.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585818/ERX585818.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585818/ERX585818.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585818/ERX585818.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 18:37:30: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:37:30: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:37:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585818/ERX585818.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585818/ERX585818.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585818/ERX585818.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585818/ERX585818.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 18:37:39: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:37:39: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:37:44: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:37:44: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:37:44: #1 total tags in treatment: 397986 INFO @ Fri, 05 Jul 2019 18:37:44: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:37:44: #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 18:37:44: #1 tags after filtering in treatment: 333047 INFO @ Fri, 05 Jul 2019 18:37:44: #1 Redundant rate of treatment: 0.16 INFO @ Fri, 05 Jul 2019 18:37:44: #1 finished! INFO @ Fri, 05 Jul 2019 18:37:44: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:37:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:37:44: #2 number of paired peaks: 352 WARNING @ Fri, 05 Jul 2019 18:37:44: Fewer paired peaks (352) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 352 pairs to build model! INFO @ Fri, 05 Jul 2019 18:37:44: start model_add_line... INFO @ Fri, 05 Jul 2019 18:37:44: start X-correlation... INFO @ Fri, 05 Jul 2019 18:37:44: end of X-cor INFO @ Fri, 05 Jul 2019 18:37:44: #2 finished! INFO @ Fri, 05 Jul 2019 18:37:44: #2 predicted fragment length is 268 bps INFO @ Fri, 05 Jul 2019 18:37:44: #2 alternative fragment length(s) may be 43,59,92,132,182,220,268,310,365,424,489,520,572 bps INFO @ Fri, 05 Jul 2019 18:37:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585818/ERX585818.05_model.r INFO @ Fri, 05 Jul 2019 18:37:44: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:37:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:37:44: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:37:44: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:37:44: #1 total tags in treatment: 397986 INFO @ Fri, 05 Jul 2019 18:37:44: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:37:44: #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 18:37:44: #1 tags after filtering in treatment: 333047 INFO @ Fri, 05 Jul 2019 18:37:44: #1 Redundant rate of treatment: 0.16 INFO @ Fri, 05 Jul 2019 18:37:44: #1 finished! INFO @ Fri, 05 Jul 2019 18:37:44: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:37:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:37:44: #2 number of paired peaks: 352 WARNING @ Fri, 05 Jul 2019 18:37:44: Fewer paired peaks (352) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 352 pairs to build model! INFO @ Fri, 05 Jul 2019 18:37:44: start model_add_line... INFO @ Fri, 05 Jul 2019 18:37:44: start X-correlation... INFO @ Fri, 05 Jul 2019 18:37:44: end of X-cor INFO @ Fri, 05 Jul 2019 18:37:44: #2 finished! INFO @ Fri, 05 Jul 2019 18:37:44: #2 predicted fragment length is 268 bps INFO @ Fri, 05 Jul 2019 18:37:44: #2 alternative fragment length(s) may be 43,59,92,132,182,220,268,310,365,424,489,520,572 bps INFO @ Fri, 05 Jul 2019 18:37:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585818/ERX585818.10_model.r INFO @ Fri, 05 Jul 2019 18:37:44: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:37:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:37:45: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:37:45: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585818/ERX585818.05_peaks.xls INFO @ Fri, 05 Jul 2019 18:37:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585818/ERX585818.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:37:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585818/ERX585818.05_summits.bed INFO @ Fri, 05 Jul 2019 18:37:45: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (109 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 18:37:46: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:37:46: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:37:46: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:37:46: #1 total tags in treatment: 397986 INFO @ Fri, 05 Jul 2019 18:37:46: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:37:46: #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 18:37:46: #1 tags after filtering in treatment: 333047 INFO @ Fri, 05 Jul 2019 18:37:46: #1 Redundant rate of treatment: 0.16 INFO @ Fri, 05 Jul 2019 18:37:46: #1 finished! INFO @ Fri, 05 Jul 2019 18:37:46: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:37:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:37:46: #2 number of paired peaks: 352 WARNING @ Fri, 05 Jul 2019 18:37:46: Fewer paired peaks (352) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 352 pairs to build model! INFO @ Fri, 05 Jul 2019 18:37:46: start model_add_line... INFO @ Fri, 05 Jul 2019 18:37:46: start X-correlation... INFO @ Fri, 05 Jul 2019 18:37:46: end of X-cor INFO @ Fri, 05 Jul 2019 18:37:46: #2 finished! INFO @ Fri, 05 Jul 2019 18:37:46: #2 predicted fragment length is 268 bps INFO @ Fri, 05 Jul 2019 18:37:46: #2 alternative fragment length(s) may be 43,59,92,132,182,220,268,310,365,424,489,520,572 bps INFO @ Fri, 05 Jul 2019 18:37:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585818/ERX585818.20_model.r INFO @ Fri, 05 Jul 2019 18:37:46: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:37:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:37:46: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585818/ERX585818.10_peaks.xls INFO @ Fri, 05 Jul 2019 18:37:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585818/ERX585818.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:37:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585818/ERX585818.10_summits.bed INFO @ Fri, 05 Jul 2019 18:37:46: Done! CompletedMACS2peakCalling pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (24 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 18:37:47: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:37:48: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585818/ERX585818.20_peaks.xls BedGraph に変換しました。 INFO @ Fri, 05 Jul 2019 18:38:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585818/ERX585818.20_peaks.narrowPeak BigWig に変換中... INFO @ Fri, 05 Jul 2019 18:38:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585818/ERX585818.20_summits.bed INFO @ Fri, 05 Jul 2019 18:38:15: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。 CompletedMACS2peakCalling