Job ID = 2008254 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 987,417 reads read : 1,974,834 reads written : 1,974,834 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR628974.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: 00:10:44 987417 reads; of these: 987417 (100.00%) were paired; of these: 14355 (1.45%) aligned concordantly 0 times 884227 (89.55%) aligned concordantly exactly 1 time 88835 (9.00%) aligned concordantly >1 times ---- 14355 pairs aligned concordantly 0 times; of these: 7281 (50.72%) aligned discordantly 1 time ---- 7074 pairs aligned 0 times concordantly or discordantly; of these: 14148 mates make up the pairs; of these: 8114 (57.35%) aligned 0 times 3860 (27.28%) aligned exactly 1 time 2174 (15.37%) aligned >1 times 99.59% overall alignment rate Time searching: 00:10:44 Overall time: 00:10:44 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] 896386 / 978426 = 0.9162 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 18:18:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585777/ERX585777.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585777/ERX585777.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585777/ERX585777.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585777/ERX585777.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 18:18:11: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:18:11: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:18:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585777/ERX585777.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585777/ERX585777.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585777/ERX585777.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585777/ERX585777.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 18:18:11: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:18:11: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:18:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585777/ERX585777.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585777/ERX585777.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585777/ERX585777.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585777/ERX585777.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 18:18:11: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:18:11: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:18:12: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:18:12: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:18:12: #1 total tags in treatment: 82260 INFO @ Fri, 05 Jul 2019 18:18:12: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:18:12: #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 18:18:12: #1 tags after filtering in treatment: 76814 INFO @ Fri, 05 Jul 2019 18:18:12: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 18:18:12: #1 finished! INFO @ Fri, 05 Jul 2019 18:18:12: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:18:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:18:12: #2 number of paired peaks: 218 WARNING @ Fri, 05 Jul 2019 18:18:12: Fewer paired peaks (218) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 218 pairs to build model! INFO @ Fri, 05 Jul 2019 18:18:12: start model_add_line... INFO @ Fri, 05 Jul 2019 18:18:12: start X-correlation... INFO @ Fri, 05 Jul 2019 18:18:12: end of X-cor INFO @ Fri, 05 Jul 2019 18:18:12: #2 finished! INFO @ Fri, 05 Jul 2019 18:18:12: #2 predicted fragment length is 161 bps INFO @ Fri, 05 Jul 2019 18:18:12: #2 alternative fragment length(s) may be 14,126,161,183,208,246,265,312,483,520,542,577 bps INFO @ Fri, 05 Jul 2019 18:18:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585777/ERX585777.05_model.r INFO @ Fri, 05 Jul 2019 18:18:12: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:18:12: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:18:12: #1 total tags in treatment: 82260 INFO @ Fri, 05 Jul 2019 18:18:12: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:18:12: #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 18:18:12: #1 tags after filtering in treatment: 76814 INFO @ Fri, 05 Jul 2019 18:18:12: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 18:18:12: #1 finished! INFO @ Fri, 05 Jul 2019 18:18:12: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:18:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:18:12: #2 number of paired peaks: 218 WARNING @ Fri, 05 Jul 2019 18:18:12: Fewer paired peaks (218) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 218 pairs to build model! INFO @ Fri, 05 Jul 2019 18:18:12: start model_add_line... INFO @ Fri, 05 Jul 2019 18:18:12: start X-correlation... INFO @ Fri, 05 Jul 2019 18:18:12: end of X-cor INFO @ Fri, 05 Jul 2019 18:18:12: #2 finished! INFO @ Fri, 05 Jul 2019 18:18:12: #2 predicted fragment length is 161 bps INFO @ Fri, 05 Jul 2019 18:18:12: #2 alternative fragment length(s) may be 14,126,161,183,208,246,265,312,483,520,542,577 bps INFO @ Fri, 05 Jul 2019 18:18:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585777/ERX585777.10_model.r INFO @ Fri, 05 Jul 2019 18:18:13: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:18:13: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:18:13: #1 total tags in treatment: 82260 INFO @ Fri, 05 Jul 2019 18:18:13: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:18:13: #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 18:18:13: #1 tags after filtering in treatment: 76814 INFO @ Fri, 05 Jul 2019 18:18:13: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 18:18:13: #1 finished! INFO @ Fri, 05 Jul 2019 18:18:13: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:18:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:18:13: #2 number of paired peaks: 218 WARNING @ Fri, 05 Jul 2019 18:18:13: Fewer paired peaks (218) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 218 pairs to build model! INFO @ Fri, 05 Jul 2019 18:18:13: start model_add_line... INFO @ Fri, 05 Jul 2019 18:18:13: start X-correlation... INFO @ Fri, 05 Jul 2019 18:18:13: end of X-cor INFO @ Fri, 05 Jul 2019 18:18:13: #2 finished! INFO @ Fri, 05 Jul 2019 18:18:13: #2 predicted fragment length is 161 bps INFO @ Fri, 05 Jul 2019 18:18:13: #2 alternative fragment length(s) may be 14,126,161,183,208,246,265,312,483,520,542,577 bps INFO @ Fri, 05 Jul 2019 18:18:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585777/ERX585777.20_model.r INFO @ Fri, 05 Jul 2019 18:18:31: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:18:31: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:18:31: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:18:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:18:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:18:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:19:04: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:19:04: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:19:04: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:19:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585777/ERX585777.20_peaks.xls INFO @ Fri, 05 Jul 2019 18:19:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585777/ERX585777.10_peaks.xls INFO @ Fri, 05 Jul 2019 18:19:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585777/ERX585777.05_peaks.xls BedGraph に変換しました。 INFO @ Fri, 05 Jul 2019 18:19:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585777/ERX585777.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:19:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585777/ERX585777.10_peaks.narrowPeak BigWig に変換中... INFO @ Fri, 05 Jul 2019 18:19:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585777/ERX585777.20_summits.bed INFO @ Fri, 05 Jul 2019 18:19:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585777/ERX585777.10_summits.bed INFO @ Fri, 05 Jul 2019 18:19:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585777/ERX585777.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:19:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585777/ERX585777.05_summits.bed INFO @ Fri, 05 Jul 2019 18:19:36: Done! INFO @ Fri, 05 Jul 2019 18:19:36: Done! INFO @ Fri, 05 Jul 2019 18:19:36: Done! BigWig に変換しました。 pass1 - making usageList (0 chroms)pass1 - making usageList (8 chroms)pass1 - making usageList (0 chroms): 1 millis : 1 millis : 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184)needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass2 - checking and writing primary data (13 records, 4 fields): 9 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling