Job ID = 2641230 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 4,459,642 reads read : 8,919,284 reads written : 8,919,284 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: 00:02:08 4459642 reads; of these: 4459642 (100.00%) were paired; of these: 2406747 (53.97%) aligned concordantly 0 times 1687933 (37.85%) aligned concordantly exactly 1 time 364962 (8.18%) aligned concordantly >1 times ---- 2406747 pairs aligned concordantly 0 times; of these: 205925 (8.56%) aligned discordantly 1 time ---- 2200822 pairs aligned 0 times concordantly or discordantly; of these: 4401644 mates make up the pairs; of these: 3838391 (87.20%) aligned 0 times 418278 (9.50%) aligned exactly 1 time 144975 (3.29%) aligned >1 times 56.97% overall alignment rate Time searching: 00:02:08 Overall time: 00:02:08 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] 304664 / 2196178 = 0.1387 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:08:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5820064/SRX5820064.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5820064/SRX5820064.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5820064/SRX5820064.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5820064/SRX5820064.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 @ Sat, 24 Aug 2019 22:08:46: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:08:46: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:08:53: 1000000 INFO @ Sat, 24 Aug 2019 22:08:59: 2000000 INFO @ Sat, 24 Aug 2019 22:09:06: 3000000 INFO @ Sat, 24 Aug 2019 22:09:12: 4000000 INFO @ Sat, 24 Aug 2019 22:09:15: #1 tag size is determined as 39 bps INFO @ Sat, 24 Aug 2019 22:09:15: #1 tag size = 39 INFO @ Sat, 24 Aug 2019 22:09:15: #1 total tags in treatment: 1805524 INFO @ Sat, 24 Aug 2019 22:09:15: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:09:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:09:15: #1 tags after filtering in treatment: 1443344 INFO @ Sat, 24 Aug 2019 22:09:15: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 24 Aug 2019 22:09:15: #1 finished! INFO @ Sat, 24 Aug 2019 22:09:15: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:09:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:09:16: #2 number of paired peaks: 99 WARNING @ Sat, 24 Aug 2019 22:09:16: Too few paired peaks (99) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Sat, 24 Aug 2019 22:09:16: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5820064/SRX5820064.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5820064/SRX5820064.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5820064/SRX5820064.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5820064/SRX5820064.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:09:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5820064/SRX5820064.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5820064/SRX5820064.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5820064/SRX5820064.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5820064/SRX5820064.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 @ Sat, 24 Aug 2019 22:09:16: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:09:16: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:09:24: 1000000 INFO @ Sat, 24 Aug 2019 22:09:31: 2000000 INFO @ Sat, 24 Aug 2019 22:09:38: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:09:45: 4000000 INFO @ Sat, 24 Aug 2019 22:09:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5820064/SRX5820064.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5820064/SRX5820064.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5820064/SRX5820064.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5820064/SRX5820064.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 @ Sat, 24 Aug 2019 22:09:46: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:09:46: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:09:49: #1 tag size is determined as 39 bps INFO @ Sat, 24 Aug 2019 22:09:49: #1 tag size = 39 INFO @ Sat, 24 Aug 2019 22:09:49: #1 total tags in treatment: 1805524 INFO @ Sat, 24 Aug 2019 22:09:49: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:09:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:09:49: #1 tags after filtering in treatment: 1443344 INFO @ Sat, 24 Aug 2019 22:09:49: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 24 Aug 2019 22:09:49: #1 finished! INFO @ Sat, 24 Aug 2019 22:09:49: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:09:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:09:49: #2 number of paired peaks: 99 WARNING @ Sat, 24 Aug 2019 22:09:49: Too few paired peaks (99) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Sat, 24 Aug 2019 22:09:49: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5820064/SRX5820064.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5820064/SRX5820064.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5820064/SRX5820064.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5820064/SRX5820064.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:09:56: 1000000 INFO @ Sat, 24 Aug 2019 22:10:05: 2000000 INFO @ Sat, 24 Aug 2019 22:10:14: 3000000 INFO @ Sat, 24 Aug 2019 22:10:23: 4000000 INFO @ Sat, 24 Aug 2019 22:10:27: #1 tag size is determined as 39 bps INFO @ Sat, 24 Aug 2019 22:10:27: #1 tag size = 39 INFO @ Sat, 24 Aug 2019 22:10:27: #1 total tags in treatment: 1805524 INFO @ Sat, 24 Aug 2019 22:10:27: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:10:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:10:27: #1 tags after filtering in treatment: 1443344 INFO @ Sat, 24 Aug 2019 22:10:27: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 24 Aug 2019 22:10:27: #1 finished! INFO @ Sat, 24 Aug 2019 22:10:27: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:10:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:10:27: #2 number of paired peaks: 99 WARNING @ Sat, 24 Aug 2019 22:10:27: Too few paired peaks (99) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Sat, 24 Aug 2019 22:10:27: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5820064/SRX5820064.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5820064/SRX5820064.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5820064/SRX5820064.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5820064/SRX5820064.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。