Job ID = 2008345 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 352,598 reads read : 705,196 reads written : 705,196 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR629060.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: 00:00:18 352598 reads; of these: 352598 (100.00%) were paired; of these: 24773 (7.03%) aligned concordantly 0 times 298669 (84.71%) aligned concordantly exactly 1 time 29156 (8.27%) aligned concordantly >1 times ---- 24773 pairs aligned concordantly 0 times; of these: 4873 (19.67%) aligned discordantly 1 time ---- 19900 pairs aligned 0 times concordantly or discordantly; of these: 39800 mates make up the pairs; of these: 37923 (95.28%) aligned 0 times 1226 (3.08%) aligned exactly 1 time 651 (1.64%) aligned >1 times 94.62% overall alignment rate Time searching: 00:00:18 Overall time: 00:00:18 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] 307690 / 332280 = 0.9260 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 18:40:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585850/ERX585850.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585850/ERX585850.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585850/ERX585850.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585850/ERX585850.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 18:40:40: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:40:40: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 18:40:40: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:40:40: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:40:40: #1 total tags in treatment: 21811 INFO @ Fri, 05 Jul 2019 18:40:40: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:40:40: #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 18:40:40: #1 tags after filtering in treatment: 21169 INFO @ Fri, 05 Jul 2019 18:40:40: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 05 Jul 2019 18:40:40: #1 finished! INFO @ Fri, 05 Jul 2019 18:40:40: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:40:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:40:40: #2 number of paired peaks: 208 WARNING @ Fri, 05 Jul 2019 18:40:40: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Fri, 05 Jul 2019 18:40:40: start model_add_line... INFO @ Fri, 05 Jul 2019 18:40:40: start X-correlation... INFO @ Fri, 05 Jul 2019 18:40:40: end of X-cor INFO @ Fri, 05 Jul 2019 18:40:40: #2 finished! INFO @ Fri, 05 Jul 2019 18:40:40: #2 predicted fragment length is 300 bps INFO @ Fri, 05 Jul 2019 18:40:40: #2 alternative fragment length(s) may be 17,44,78,174,206,230,263,300,380,417,476,532 bps INFO @ Fri, 05 Jul 2019 18:40:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585850/ERX585850.05_model.r INFO @ Fri, 05 Jul 2019 18:40:40: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:40:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:40:40: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:40:40: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585850/ERX585850.05_peaks.xls INFO @ Fri, 05 Jul 2019 18:40:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585850/ERX585850.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:40:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585850/ERX585850.05_summits.bed INFO @ Fri, 05 Jul 2019 18:40:40: 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 18:40:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585850/ERX585850.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585850/ERX585850.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585850/ERX585850.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585850/ERX585850.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 18:40:41: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:40:41: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:40:41: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:40:41: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:40:41: #1 total tags in treatment: 21811 INFO @ Fri, 05 Jul 2019 18:40:41: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:40:41: #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 18:40:41: #1 tags after filtering in treatment: 21169 INFO @ Fri, 05 Jul 2019 18:40:41: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 05 Jul 2019 18:40:41: #1 finished! INFO @ Fri, 05 Jul 2019 18:40:41: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:40:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:40:41: #2 number of paired peaks: 208 WARNING @ Fri, 05 Jul 2019 18:40:41: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Fri, 05 Jul 2019 18:40:41: start model_add_line... INFO @ Fri, 05 Jul 2019 18:40:41: start X-correlation... INFO @ Fri, 05 Jul 2019 18:40:41: end of X-cor INFO @ Fri, 05 Jul 2019 18:40:41: #2 finished! INFO @ Fri, 05 Jul 2019 18:40:41: #2 predicted fragment length is 300 bps INFO @ Fri, 05 Jul 2019 18:40:41: #2 alternative fragment length(s) may be 17,44,78,174,206,230,263,300,380,417,476,532 bps INFO @ Fri, 05 Jul 2019 18:40:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585850/ERX585850.10_model.r INFO @ Fri, 05 Jul 2019 18:40:41: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:40:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:40:41: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:40:41: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585850/ERX585850.10_peaks.xls INFO @ Fri, 05 Jul 2019 18:40:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585850/ERX585850.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585850/ERX585850.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585850/ERX585850.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585850/ERX585850.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 18:40:42: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:40:42: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:40:42: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:40:42: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:40:42: #1 total tags in treatment: 21811 INFO @ Fri, 05 Jul 2019 18:40:42: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:40:42: #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 18:40:42: #1 tags after filtering in treatment: 21169 INFO @ Fri, 05 Jul 2019 18:40:42: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 05 Jul 2019 18:40:42: #1 finished! INFO @ Fri, 05 Jul 2019 18:40:42: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:40:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:40:42: #2 number of paired peaks: 208 WARNING @ Fri, 05 Jul 2019 18:40:42: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Fri, 05 Jul 2019 18:40:42: start model_add_line... INFO @ Fri, 05 Jul 2019 18:40:42: start X-correlation... INFO @ Fri, 05 Jul 2019 18:40:42: end of X-cor INFO @ Fri, 05 Jul 2019 18:40:42: #2 finished! INFO @ Fri, 05 Jul 2019 18:40:42: #2 predicted fragment length is 300 bps INFO @ Fri, 05 Jul 2019 18:40:42: #2 alternative fragment length(s) may be 17,44,78,174,206,230,263,300,380,417,476,532 bps INFO @ Fri, 05 Jul 2019 18:40:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585850/ERX585850.20_model.r INFO @ Fri, 05 Jul 2019 18:41:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585850/ERX585850.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:41:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585850/ERX585850.10_summits.bed INFO @ Fri, 05 Jul 2019 18:41:05: Done! INFO @ Fri, 05 Jul 2019 18:41:05: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:41:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:41:05: #3 Call peaks for each chromosome... pass1 - making usageList (0 chroms): 7 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) INFO @ Fri, 05 Jul 2019 18:41:06: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585850/ERX585850.20_peaks.xls INFO @ Fri, 05 Jul 2019 18:41:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585850/ERX585850.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:41:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585850/ERX585850.20_summits.bed INFO @ Fri, 05 Jul 2019 18:41:06: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling CompletedMACS2peakCalling