Job ID = 2008316 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 14,453,099 reads read : 28,906,198 reads written : 28,906,198 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR629045.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: 00:11:18 14453099 reads; of these: 14453099 (100.00%) were paired; of these: 733514 (5.08%) aligned concordantly 0 times 12585606 (87.08%) aligned concordantly exactly 1 time 1133979 (7.85%) aligned concordantly >1 times ---- 733514 pairs aligned concordantly 0 times; of these: 159872 (21.80%) aligned discordantly 1 time ---- 573642 pairs aligned 0 times concordantly or discordantly; of these: 1147284 mates make up the pairs; of these: 1033858 (90.11%) aligned 0 times 69120 (6.02%) aligned exactly 1 time 44306 (3.86%) aligned >1 times 96.42% overall alignment rate Time searching: 00:11:18 Overall time: 00:11:18 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_sort_core] merging from 12 files... [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] 12933379 / 13867559 = 0.9326 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 18:45:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585825/ERX585825.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585825/ERX585825.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585825/ERX585825.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585825/ERX585825.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 18:45:27: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:45:27: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:45:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585825/ERX585825.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585825/ERX585825.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585825/ERX585825.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585825/ERX585825.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 18:45:27: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:45:27: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:45:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585825/ERX585825.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585825/ERX585825.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585825/ERX585825.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585825/ERX585825.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 18:45:28: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:45:28: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:45:34: 1000000 INFO @ Fri, 05 Jul 2019 18:45:35: 1000000 INFO @ Fri, 05 Jul 2019 18:45:37: 1000000 INFO @ Fri, 05 Jul 2019 18:45:41: 2000000 INFO @ Fri, 05 Jul 2019 18:45:41: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:45:41: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:45:41: #1 total tags in treatment: 867598 INFO @ Fri, 05 Jul 2019 18:45:41: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:45:41: #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 18:45:41: #1 tags after filtering in treatment: 668349 INFO @ Fri, 05 Jul 2019 18:45:41: #1 Redundant rate of treatment: 0.23 INFO @ Fri, 05 Jul 2019 18:45:41: #1 finished! INFO @ Fri, 05 Jul 2019 18:45:41: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:45:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:45:41: #2 number of paired peaks: 244 WARNING @ Fri, 05 Jul 2019 18:45:41: Fewer paired peaks (244) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 244 pairs to build model! INFO @ Fri, 05 Jul 2019 18:45:41: start model_add_line... INFO @ Fri, 05 Jul 2019 18:45:41: start X-correlation... INFO @ Fri, 05 Jul 2019 18:45:41: end of X-cor INFO @ Fri, 05 Jul 2019 18:45:41: #2 finished! INFO @ Fri, 05 Jul 2019 18:45:41: #2 predicted fragment length is 263 bps INFO @ Fri, 05 Jul 2019 18:45:41: #2 alternative fragment length(s) may be 0,25,65,100,116,164,183,203,233,263,298,355,446,508,534,558,586 bps INFO @ Fri, 05 Jul 2019 18:45:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585825/ERX585825.10_model.r INFO @ Fri, 05 Jul 2019 18:45:41: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:45:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:45:42: 2000000 INFO @ Fri, 05 Jul 2019 18:45:42: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:45:42: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:45:42: #1 total tags in treatment: 867598 INFO @ Fri, 05 Jul 2019 18:45:42: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:45:42: #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 18:45:42: #1 tags after filtering in treatment: 668349 INFO @ Fri, 05 Jul 2019 18:45:42: #1 Redundant rate of treatment: 0.23 INFO @ Fri, 05 Jul 2019 18:45:42: #1 finished! INFO @ Fri, 05 Jul 2019 18:45:42: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:45:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:45:42: #2 number of paired peaks: 244 WARNING @ Fri, 05 Jul 2019 18:45:42: Fewer paired peaks (244) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 244 pairs to build model! INFO @ Fri, 05 Jul 2019 18:45:42: start model_add_line... INFO @ Fri, 05 Jul 2019 18:45:42: start X-correlation... INFO @ Fri, 05 Jul 2019 18:45:42: end of X-cor INFO @ Fri, 05 Jul 2019 18:45:42: #2 finished! INFO @ Fri, 05 Jul 2019 18:45:42: #2 predicted fragment length is 263 bps INFO @ Fri, 05 Jul 2019 18:45:42: #2 alternative fragment length(s) may be 0,25,65,100,116,164,183,203,233,263,298,355,446,508,534,558,586 bps INFO @ Fri, 05 Jul 2019 18:45:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585825/ERX585825.05_model.r INFO @ Fri, 05 Jul 2019 18:45:42: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:45:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:45:43: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:45:44: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585825/ERX585825.10_peaks.xls INFO @ Fri, 05 Jul 2019 18:45:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585825/ERX585825.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:45:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585825/ERX585825.10_summits.bed INFO @ Fri, 05 Jul 2019 18:45:44: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (72 records, 4 fields): 4 millis INFO @ Fri, 05 Jul 2019 18:45:45: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:45:45: 2000000 INFO @ Fri, 05 Jul 2019 18:45:45: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:45:45: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:45:45: #1 total tags in treatment: 867598 INFO @ Fri, 05 Jul 2019 18:45:45: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:45:45: #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 18:45:45: #1 tags after filtering in treatment: 668349 INFO @ Fri, 05 Jul 2019 18:45:45: #1 Redundant rate of treatment: 0.23 INFO @ Fri, 05 Jul 2019 18:45:45: #1 finished! INFO @ Fri, 05 Jul 2019 18:45:45: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:45:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:45:45: #2 number of paired peaks: 244 WARNING @ Fri, 05 Jul 2019 18:45:45: Fewer paired peaks (244) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 244 pairs to build model! INFO @ Fri, 05 Jul 2019 18:45:45: start model_add_line... INFO @ Fri, 05 Jul 2019 18:45:45: start X-correlation... INFO @ Fri, 05 Jul 2019 18:45:45: end of X-cor INFO @ Fri, 05 Jul 2019 18:45:45: #2 finished! INFO @ Fri, 05 Jul 2019 18:45:45: #2 predicted fragment length is 263 bps INFO @ Fri, 05 Jul 2019 18:45:45: #2 alternative fragment length(s) may be 0,25,65,100,116,164,183,203,233,263,298,355,446,508,534,558,586 bps INFO @ Fri, 05 Jul 2019 18:45:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585825/ERX585825.20_model.r INFO @ Fri, 05 Jul 2019 18:45:45: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:45:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:45:46: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585825/ERX585825.05_peaks.xls INFO @ Fri, 05 Jul 2019 18:45:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585825/ERX585825.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:45:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585825/ERX585825.05_summits.bed INFO @ Fri, 05 Jul 2019 18:45:46: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (142 records, 4 fields): 3 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 18:45:48: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:45:49: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585825/ERX585825.20_peaks.xls BedGraph に変換しました。 INFO @ Fri, 05 Jul 2019 18:46:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585825/ERX585825.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:46:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585825/ERX585825.20_summits.bed BigWig に変換中... INFO @ Fri, 05 Jul 2019 18:46:11: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 319 millis CompletedMACS2peakCalling BigWig に変換しました。