Job ID = 2007667 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 117,945 reads read : 235,890 reads written : 235,890 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: 00:00:04 117945 reads; of these: 117945 (100.00%) were paired; of these: 5866 (4.97%) aligned concordantly 0 times 103280 (87.57%) aligned concordantly exactly 1 time 8799 (7.46%) aligned concordantly >1 times ---- 5866 pairs aligned concordantly 0 times; of these: 2311 (39.40%) aligned discordantly 1 time ---- 3555 pairs aligned 0 times concordantly or discordantly; of these: 7110 mates make up the pairs; of these: 5409 (76.08%) aligned 0 times 1115 (15.68%) aligned exactly 1 time 586 (8.24%) aligned >1 times 97.71% 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] 139 / 114005 = 0.0012 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 16:15:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX433644/ERX433644.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX433644/ERX433644.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX433644/ERX433644.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX433644/ERX433644.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 16:15:36: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:15:36: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:15:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX433644/ERX433644.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX433644/ERX433644.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX433644/ERX433644.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX433644/ERX433644.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 16:15:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:15:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:15:37: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:15:37: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:15:37: #1 total tags in treatment: 111941 INFO @ Fri, 05 Jul 2019 16:15:37: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:15:37: #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 16:15:37: #1 tags after filtering in treatment: 111150 INFO @ Fri, 05 Jul 2019 16:15:37: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 16:15:37: #1 finished! INFO @ Fri, 05 Jul 2019 16:15:37: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:15:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:15:37: #2 number of paired peaks: 341 WARNING @ Fri, 05 Jul 2019 16:15:37: 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 16:15:37: start model_add_line... INFO @ Fri, 05 Jul 2019 16:15:37: start X-correlation... INFO @ Fri, 05 Jul 2019 16:15:38: end of X-cor INFO @ Fri, 05 Jul 2019 16:15:38: #2 finished! INFO @ Fri, 05 Jul 2019 16:15:38: #2 predicted fragment length is 204 bps INFO @ Fri, 05 Jul 2019 16:15:38: #2 alternative fragment length(s) may be 61,65,127,152,168,204,287 bps INFO @ Fri, 05 Jul 2019 16:15:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX433644/ERX433644.05_model.r INFO @ Fri, 05 Jul 2019 16:15:38: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:15:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:15:38: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:15:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX433644/ERX433644.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX433644/ERX433644.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX433644/ERX433644.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX433644/ERX433644.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 16:15:38: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:15:38: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:15:38: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX433644/ERX433644.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:15:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX433644/ERX433644.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:15:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX433644/ERX433644.05_summits.bed INFO @ Fri, 05 Jul 2019 16:15:38: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (139 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 16:15:39: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:15:39: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:15:39: #1 total tags in treatment: 111941 INFO @ Fri, 05 Jul 2019 16:15:39: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:15:39: #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 16:15:39: #1 tags after filtering in treatment: 111150 INFO @ Fri, 05 Jul 2019 16:15:39: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 16:15:39: #1 finished! INFO @ Fri, 05 Jul 2019 16:15:39: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:15:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:15:39: #2 number of paired peaks: 341 WARNING @ Fri, 05 Jul 2019 16:15:39: 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 16:15:39: start model_add_line... INFO @ Fri, 05 Jul 2019 16:15:39: start X-correlation... INFO @ Fri, 05 Jul 2019 16:15:39: end of X-cor INFO @ Fri, 05 Jul 2019 16:15:39: #2 finished! INFO @ Fri, 05 Jul 2019 16:15:39: #2 predicted fragment length is 204 bps INFO @ Fri, 05 Jul 2019 16:15:39: #2 alternative fragment length(s) may be 61,65,127,152,168,204,287 bps INFO @ Fri, 05 Jul 2019 16:15:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX433644/ERX433644.10_model.r INFO @ Fri, 05 Jul 2019 16:15:39: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:15:39: #3 Pre-compute pvalue-qvalue table... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:15:39: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:15:39: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX433644/ERX433644.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:15:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX433644/ERX433644.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:15:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX433644/ERX433644.10_summits.bed INFO @ Fri, 05 Jul 2019 16:15:39: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (35 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 16:15:39: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:15:39: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:15:39: #1 total tags in treatment: 111941 INFO @ Fri, 05 Jul 2019 16:15:39: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:15:39: #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 16:15:39: #1 tags after filtering in treatment: 111150 INFO @ Fri, 05 Jul 2019 16:15:39: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 16:15:39: #1 finished! INFO @ Fri, 05 Jul 2019 16:15:39: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:15:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:15:39: #2 number of paired peaks: 341 WARNING @ Fri, 05 Jul 2019 16:15:39: 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 16:15:39: start model_add_line... INFO @ Fri, 05 Jul 2019 16:15:39: start X-correlation... INFO @ Fri, 05 Jul 2019 16:15:39: end of X-cor INFO @ Fri, 05 Jul 2019 16:15:39: #2 finished! INFO @ Fri, 05 Jul 2019 16:15:39: #2 predicted fragment length is 204 bps INFO @ Fri, 05 Jul 2019 16:15:39: #2 alternative fragment length(s) may be 61,65,127,152,168,204,287 bps INFO @ Fri, 05 Jul 2019 16:15:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX433644/ERX433644.20_model.r INFO @ Fri, 05 Jul 2019 16:15:39: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:15:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:15:40: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:15:40: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX433644/ERX433644.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:15:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX433644/ERX433644.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:15:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX433644/ERX433644.20_summits.bed INFO @ Fri, 05 Jul 2019 16:15:40: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (4 records, 4 fields): 2 millis BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 CompletedMACS2peakCalling CompletedMACS2peakCalling