Job ID = 2008168 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 683,839 reads read : 1,367,678 reads written : 1,367,678 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: 00:00:30 683839 reads; of these: 683839 (100.00%) were paired; of these: 55174 (8.07%) aligned concordantly 0 times 573138 (83.81%) aligned concordantly exactly 1 time 55527 (8.12%) aligned concordantly >1 times ---- 55174 pairs aligned concordantly 0 times; of these: 10822 (19.61%) aligned discordantly 1 time ---- 44352 pairs aligned 0 times concordantly or discordantly; of these: 88704 mates make up the pairs; of these: 85203 (96.05%) aligned 0 times 2279 (2.57%) aligned exactly 1 time 1222 (1.38%) aligned >1 times 93.77% 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] 580340 / 638917 = 0.9083 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 17:32:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585705/ERX585705.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585705/ERX585705.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585705/ERX585705.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585705/ERX585705.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 17:32:46: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:32:46: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:32:46: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 17:32:46: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 17:32:46: #1 total tags in treatment: 51780 INFO @ Fri, 05 Jul 2019 17:32:46: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:32:46: #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 17:32:46: #1 tags after filtering in treatment: 50153 INFO @ Fri, 05 Jul 2019 17:32:46: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 05 Jul 2019 17:32:46: #1 finished! INFO @ Fri, 05 Jul 2019 17:32:46: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:32:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:32:46: #2 number of paired peaks: 155 WARNING @ Fri, 05 Jul 2019 17:32:46: Fewer paired peaks (155) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 155 pairs to build model! INFO @ Fri, 05 Jul 2019 17:32:46: start model_add_line... INFO @ Fri, 05 Jul 2019 17:32:46: start X-correlation... INFO @ Fri, 05 Jul 2019 17:32:46: end of X-cor INFO @ Fri, 05 Jul 2019 17:32:46: #2 finished! INFO @ Fri, 05 Jul 2019 17:32:46: #2 predicted fragment length is 249 bps INFO @ Fri, 05 Jul 2019 17:32:46: #2 alternative fragment length(s) may be 4,34,76,98,117,145,172,207,227,249,267,306,389,397,412,465,537,582 bps INFO @ Fri, 05 Jul 2019 17:32:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585705/ERX585705.05_model.r INFO @ Fri, 05 Jul 2019 17:32:46: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:32:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:32:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585705/ERX585705.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585705/ERX585705.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585705/ERX585705.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585705/ERX585705.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 17:32:47: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:32:47: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:32:47: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:32:47: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585705/ERX585705.05_peaks.xls INFO @ Fri, 05 Jul 2019 17:32:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585705/ERX585705.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:32:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585705/ERX585705.05_summits.bed INFO @ Fri, 05 Jul 2019 17:32:47: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 17:32:47: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 17:32:47: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 17:32:47: #1 total tags in treatment: 51780 INFO @ Fri, 05 Jul 2019 17:32:47: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:32:47: #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 17:32:47: #1 tags after filtering in treatment: 50153 INFO @ Fri, 05 Jul 2019 17:32:47: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 05 Jul 2019 17:32:47: #1 finished! INFO @ Fri, 05 Jul 2019 17:32:47: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:32:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:32:47: #2 number of paired peaks: 155 WARNING @ Fri, 05 Jul 2019 17:32:47: Fewer paired peaks (155) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 155 pairs to build model! INFO @ Fri, 05 Jul 2019 17:32:47: start model_add_line... INFO @ Fri, 05 Jul 2019 17:32:47: start X-correlation... INFO @ Fri, 05 Jul 2019 17:32:47: end of X-cor INFO @ Fri, 05 Jul 2019 17:32:47: #2 finished! INFO @ Fri, 05 Jul 2019 17:32:47: #2 predicted fragment length is 249 bps INFO @ Fri, 05 Jul 2019 17:32:47: #2 alternative fragment length(s) may be 4,34,76,98,117,145,172,207,227,249,267,306,389,397,412,465,537,582 bps INFO @ Fri, 05 Jul 2019 17:32:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585705/ERX585705.10_model.r INFO @ Fri, 05 Jul 2019 17:32:47: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:32:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:32:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585705/ERX585705.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585705/ERX585705.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585705/ERX585705.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585705/ERX585705.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 17:32:48: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:32:48: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:32:48: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:32:48: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585705/ERX585705.10_peaks.xls INFO @ Fri, 05 Jul 2019 17:32:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585705/ERX585705.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:32:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585705/ERX585705.10_summits.bed INFO @ Fri, 05 Jul 2019 17:32:48: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) BigWig に変換しました。 CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:32:48: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 17:32:48: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 17:32:48: #1 total tags in treatment: 51780 INFO @ Fri, 05 Jul 2019 17:32:48: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:32:48: #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 17:32:48: #1 tags after filtering in treatment: 50153 INFO @ Fri, 05 Jul 2019 17:32:48: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 05 Jul 2019 17:32:48: #1 finished! INFO @ Fri, 05 Jul 2019 17:32:48: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:32:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:32:49: #2 number of paired peaks: 155 WARNING @ Fri, 05 Jul 2019 17:32:49: Fewer paired peaks (155) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 155 pairs to build model! INFO @ Fri, 05 Jul 2019 17:32:49: start model_add_line... INFO @ Fri, 05 Jul 2019 17:32:49: start X-correlation... INFO @ Fri, 05 Jul 2019 17:32:49: end of X-cor INFO @ Fri, 05 Jul 2019 17:32:49: #2 finished! INFO @ Fri, 05 Jul 2019 17:32:49: #2 predicted fragment length is 249 bps INFO @ Fri, 05 Jul 2019 17:32:49: #2 alternative fragment length(s) may be 4,34,76,98,117,145,172,207,227,249,267,306,389,397,412,465,537,582 bps INFO @ Fri, 05 Jul 2019 17:32:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585705/ERX585705.20_model.r INFO @ Fri, 05 Jul 2019 17:32:49: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:32:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:32:49: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:32:49: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585705/ERX585705.20_peaks.xls INFO @ Fri, 05 Jul 2019 17:32:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585705/ERX585705.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:32:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585705/ERX585705.20_summits.bed INFO @ Fri, 05 Jul 2019 17:32:49: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling