Job ID = 2007794 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 32,498 reads read : 64,996 reads written : 64,996 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: 00:00:02 32498 reads; of these: 32498 (100.00%) were paired; of these: 3374 (10.38%) aligned concordantly 0 times 26694 (82.14%) aligned concordantly exactly 1 time 2430 (7.48%) aligned concordantly >1 times ---- 3374 pairs aligned concordantly 0 times; of these: 2002 (59.34%) aligned discordantly 1 time ---- 1372 pairs aligned 0 times concordantly or discordantly; of these: 2744 mates make up the pairs; of these: 1708 (62.24%) aligned 0 times 592 (21.57%) aligned exactly 1 time 444 (16.18%) aligned >1 times 97.37% overall alignment rate Time searching: 00:00:02 Overall time: 00:00:02 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] 39 / 30677 = 0.0013 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 16:29:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX433715/ERX433715.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX433715/ERX433715.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX433715/ERX433715.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX433715/ERX433715.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 16:29:22: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:29:22: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:29:22: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:29:22: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:29:22: #1 total tags in treatment: 29087 INFO @ Fri, 05 Jul 2019 16:29:22: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:29:22: #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 16:29:22: #1 tags after filtering in treatment: 29026 INFO @ Fri, 05 Jul 2019 16:29:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:29:22: #1 finished! INFO @ Fri, 05 Jul 2019 16:29:22: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:29:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:29:22: #2 number of paired peaks: 210 WARNING @ Fri, 05 Jul 2019 16:29:22: Fewer paired peaks (210) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 210 pairs to build model! INFO @ Fri, 05 Jul 2019 16:29:22: start model_add_line... INFO @ Fri, 05 Jul 2019 16:29:22: start X-correlation... INFO @ Fri, 05 Jul 2019 16:29:22: end of X-cor INFO @ Fri, 05 Jul 2019 16:29:22: #2 finished! INFO @ Fri, 05 Jul 2019 16:29:22: #2 predicted fragment length is 283 bps INFO @ Fri, 05 Jul 2019 16:29:22: #2 alternative fragment length(s) may be 25,157,182,217,248,283,314,336,411,494,518,539 bps INFO @ Fri, 05 Jul 2019 16:29:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX433715/ERX433715.05_model.r INFO @ Fri, 05 Jul 2019 16:29:22: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:29:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:29:22: #3 Call peaks for each chromosome... BedGraph に変換しました。 INFO @ Fri, 05 Jul 2019 16:29:22: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX433715/ERX433715.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:29:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX433715/ERX433715.05_peaks.narrowPeak BigWig に変換中... INFO @ Fri, 05 Jul 2019 16:29:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX433715/ERX433715.05_summits.bed INFO @ Fri, 05 Jul 2019 16:29:22: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis INFO @ Fri, 05 Jul 2019 16:29:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX433715/ERX433715.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX433715/ERX433715.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX433715/ERX433715.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX433715/ERX433715.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 16:29:23: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:29:23: #1 read treatment tags... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 16:29:23: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:29:23: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:29:23: #1 total tags in treatment: 29087 INFO @ Fri, 05 Jul 2019 16:29:23: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:29:23: #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 16:29:23: #1 tags after filtering in treatment: 29026 INFO @ Fri, 05 Jul 2019 16:29:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:29:23: #1 finished! INFO @ Fri, 05 Jul 2019 16:29:23: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:29:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:29:23: #2 number of paired peaks: 210 WARNING @ Fri, 05 Jul 2019 16:29:23: Fewer paired peaks (210) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 210 pairs to build model! INFO @ Fri, 05 Jul 2019 16:29:23: start model_add_line... INFO @ Fri, 05 Jul 2019 16:29:23: start X-correlation... INFO @ Fri, 05 Jul 2019 16:29:23: end of X-cor INFO @ Fri, 05 Jul 2019 16:29:23: #2 finished! INFO @ Fri, 05 Jul 2019 16:29:23: #2 predicted fragment length is 283 bps INFO @ Fri, 05 Jul 2019 16:29:23: #2 alternative fragment length(s) may be 25,157,182,217,248,283,314,336,411,494,518,539 bps INFO @ Fri, 05 Jul 2019 16:29:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX433715/ERX433715.10_model.r INFO @ Fri, 05 Jul 2019 16:29:23: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:29:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:29:23: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:29:23: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX433715/ERX433715.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:29:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX433715/ERX433715.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:29:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX433715/ERX433715.10_summits.bed INFO @ Fri, 05 Jul 2019 16:29:23: Done! CompletedMACS2peakCalling pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) INFO @ Fri, 05 Jul 2019 16:29:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX433715/ERX433715.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX433715/ERX433715.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX433715/ERX433715.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX433715/ERX433715.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 16:29:24: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:29:24: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:29:24: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:29:24: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:29:24: #1 total tags in treatment: 29087 INFO @ Fri, 05 Jul 2019 16:29:24: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:29:24: #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 16:29:24: #1 tags after filtering in treatment: 29026 INFO @ Fri, 05 Jul 2019 16:29:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:29:24: #1 finished! INFO @ Fri, 05 Jul 2019 16:29:24: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:29:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:29:24: #2 number of paired peaks: 210 WARNING @ Fri, 05 Jul 2019 16:29:24: Fewer paired peaks (210) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 210 pairs to build model! INFO @ Fri, 05 Jul 2019 16:29:24: start model_add_line... INFO @ Fri, 05 Jul 2019 16:29:24: start X-correlation... INFO @ Fri, 05 Jul 2019 16:29:24: end of X-cor INFO @ Fri, 05 Jul 2019 16:29:24: #2 finished! INFO @ Fri, 05 Jul 2019 16:29:24: #2 predicted fragment length is 283 bps INFO @ Fri, 05 Jul 2019 16:29:24: #2 alternative fragment length(s) may be 25,157,182,217,248,283,314,336,411,494,518,539 bps INFO @ Fri, 05 Jul 2019 16:29:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX433715/ERX433715.20_model.r INFO @ Fri, 05 Jul 2019 16:29:24: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:29:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:29:24: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:29:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX433715/ERX433715.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:29:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX433715/ERX433715.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:29:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX433715/ERX433715.20_summits.bed INFO @ Fri, 05 Jul 2019 16:29:24: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling CompletedMACS2peakCalling