Job ID = 2007892 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 183,483 reads read : 366,966 reads written : 366,966 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: 00:00:06 183483 reads; of these: 183483 (100.00%) were paired; of these: 36025 (19.63%) aligned concordantly 0 times 133101 (72.54%) aligned concordantly exactly 1 time 14357 (7.82%) aligned concordantly >1 times ---- 36025 pairs aligned concordantly 0 times; of these: 4176 (11.59%) aligned discordantly 1 time ---- 31849 pairs aligned 0 times concordantly or discordantly; of these: 63698 mates make up the pairs; of these: 60966 (95.71%) aligned 0 times 1544 (2.42%) aligned exactly 1 time 1188 (1.87%) aligned >1 times 83.39% overall alignment rate Time searching: 00:00:06 Overall time: 00:00:06 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] 3632 / 151158 = 0.0240 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 16:38:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX462427/ERX462427.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX462427/ERX462427.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX462427/ERX462427.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX462427/ERX462427.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 16:38:32: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:38:32: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:38:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX462427/ERX462427.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX462427/ERX462427.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX462427/ERX462427.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX462427/ERX462427.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 16:38:33: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:38:33: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:38:34: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:38:34: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:38:34: #1 total tags in treatment: 143901 INFO @ Fri, 05 Jul 2019 16:38:34: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:38:34: #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 16:38:34: #1 tags after filtering in treatment: 142968 INFO @ Fri, 05 Jul 2019 16:38:34: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 16:38:34: #1 finished! INFO @ Fri, 05 Jul 2019 16:38:34: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:38:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:38:34: #2 number of paired peaks: 154 WARNING @ Fri, 05 Jul 2019 16:38:34: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Fri, 05 Jul 2019 16:38:34: start model_add_line... INFO @ Fri, 05 Jul 2019 16:38:34: start X-correlation... INFO @ Fri, 05 Jul 2019 16:38:34: end of X-cor INFO @ Fri, 05 Jul 2019 16:38:34: #2 finished! INFO @ Fri, 05 Jul 2019 16:38:34: #2 predicted fragment length is 302 bps INFO @ Fri, 05 Jul 2019 16:38:34: #2 alternative fragment length(s) may be 35,86,117,143,168,206,228,262,284,302,324,383,407,422,442,466,503,531,550,583 bps INFO @ Fri, 05 Jul 2019 16:38:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX462427/ERX462427.05_model.r INFO @ Fri, 05 Jul 2019 16:38:34: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:38:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:38:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX462427/ERX462427.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX462427/ERX462427.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX462427/ERX462427.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX462427/ERX462427.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 16:38:34: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:38:34: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:38:35: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:38:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX462427/ERX462427.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:38:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX462427/ERX462427.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:38:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX462427/ERX462427.05_summits.bed INFO @ Fri, 05 Jul 2019 16:38:35: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (3 records, 4 fields): 1 millis INFO @ Fri, 05 Jul 2019 16:38:35: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:38:35: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:38:35: #1 total tags in treatment: 143901 INFO @ Fri, 05 Jul 2019 16:38:35: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:38:35: #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 16:38:35: #1 tags after filtering in treatment: 142968 INFO @ Fri, 05 Jul 2019 16:38:35: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 16:38:35: #1 finished! INFO @ Fri, 05 Jul 2019 16:38:35: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:38:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:38:35: #2 number of paired peaks: 154 WARNING @ Fri, 05 Jul 2019 16:38:35: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Fri, 05 Jul 2019 16:38:35: start model_add_line... INFO @ Fri, 05 Jul 2019 16:38:35: start X-correlation... INFO @ Fri, 05 Jul 2019 16:38:35: end of X-cor INFO @ Fri, 05 Jul 2019 16:38:35: #2 finished! INFO @ Fri, 05 Jul 2019 16:38:35: #2 predicted fragment length is 302 bps INFO @ Fri, 05 Jul 2019 16:38:35: #2 alternative fragment length(s) may be 35,86,117,143,168,206,228,262,284,302,324,383,407,422,442,466,503,531,550,583 bps INFO @ Fri, 05 Jul 2019 16:38:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX462427/ERX462427.10_model.r INFO @ Fri, 05 Jul 2019 16:38:35: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:38:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:38:36: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:38:36: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX462427/ERX462427.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:38:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX462427/ERX462427.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:38:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX462427/ERX462427.10_summits.bed INFO @ Fri, 05 Jul 2019 16:38:36: Done! INFO @ Fri, 05 Jul 2019 16:38:36: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:38:36: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:38:36: #1 total tags in treatment: 143901 INFO @ Fri, 05 Jul 2019 16:38:36: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:38:36: #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 16:38:36: #1 tags after filtering in treatment: 142968 INFO @ Fri, 05 Jul 2019 16:38:36: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 16:38:36: #1 finished! INFO @ Fri, 05 Jul 2019 16:38:36: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:38:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:38:36: #2 number of paired peaks: 154 WARNING @ Fri, 05 Jul 2019 16:38:36: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Fri, 05 Jul 2019 16:38:36: start model_add_line... INFO @ Fri, 05 Jul 2019 16:38:36: start X-correlation... INFO @ Fri, 05 Jul 2019 16:38:36: end of X-cor INFO @ Fri, 05 Jul 2019 16:38:36: #2 finished! INFO @ Fri, 05 Jul 2019 16:38:36: #2 predicted fragment length is 302 bps INFO @ Fri, 05 Jul 2019 16:38:36: #2 alternative fragment length(s) may be 35,86,117,143,168,206,228,262,284,302,324,383,407,422,442,466,503,531,550,583 bps INFO @ Fri, 05 Jul 2019 16:38:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX462427/ERX462427.20_model.r INFO @ Fri, 05 Jul 2019 16:38:36: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:38:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:38:37: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:38:37: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX462427/ERX462427.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:38:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX462427/ERX462427.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:38:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX462427/ERX462427.20_summits.bed INFO @ Fri, 05 Jul 2019 16:38:37: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。