Job ID = 2641223 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 8,346,732 reads read : 16,693,464 reads written : 16,693,464 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: 00:02:38 8346732 reads; of these: 8346732 (100.00%) were paired; of these: 7768885 (93.08%) aligned concordantly 0 times 496114 (5.94%) aligned concordantly exactly 1 time 81733 (0.98%) aligned concordantly >1 times ---- 7768885 pairs aligned concordantly 0 times; of these: 290292 (3.74%) aligned discordantly 1 time ---- 7478593 pairs aligned 0 times concordantly or discordantly; of these: 14957186 mates make up the pairs; of these: 12401275 (82.91%) aligned 0 times 2230338 (14.91%) aligned exactly 1 time 325573 (2.18%) aligned >1 times 25.71% overall alignment rate Time searching: 00:02:38 Overall time: 00:02:38 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] 236115 / 845148 = 0.2794 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 21:58:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5820057/SRX5820057.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5820057/SRX5820057.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5820057/SRX5820057.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5820057/SRX5820057.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 21:58:26: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:58:26: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:58:32: 1000000 INFO @ Sat, 24 Aug 2019 21:58:37: 2000000 INFO @ Sat, 24 Aug 2019 21:58:43: 3000000 INFO @ Sat, 24 Aug 2019 21:58:47: #1 tag size is determined as 45 bps INFO @ Sat, 24 Aug 2019 21:58:47: #1 tag size = 45 INFO @ Sat, 24 Aug 2019 21:58:47: #1 total tags in treatment: 436068 INFO @ Sat, 24 Aug 2019 21:58:47: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:58:47: #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 21:58:47: #1 tags after filtering in treatment: 413584 INFO @ Sat, 24 Aug 2019 21:58:47: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 24 Aug 2019 21:58:47: #1 finished! INFO @ Sat, 24 Aug 2019 21:58:47: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:58:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:58:47: #2 number of paired peaks: 69 WARNING @ Sat, 24 Aug 2019 21:58:47: Too few paired peaks (69) 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 21:58:47: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5820057/SRX5820057.05_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/SRX5820057/SRX5820057.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5820057/SRX5820057.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5820057/SRX5820057.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:58:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5820057/SRX5820057.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5820057/SRX5820057.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5820057/SRX5820057.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5820057/SRX5820057.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 21:58:56: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:58:56: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:59:02: 1000000 INFO @ Sat, 24 Aug 2019 21:59:08: 2000000 INFO @ Sat, 24 Aug 2019 21:59:14: 3000000 INFO @ Sat, 24 Aug 2019 21:59:18: #1 tag size is determined as 45 bps INFO @ Sat, 24 Aug 2019 21:59:18: #1 tag size = 45 INFO @ Sat, 24 Aug 2019 21:59:18: #1 total tags in treatment: 436068 INFO @ Sat, 24 Aug 2019 21:59:18: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:59:18: #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 21:59:18: #1 tags after filtering in treatment: 413584 INFO @ Sat, 24 Aug 2019 21:59:18: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 24 Aug 2019 21:59:18: #1 finished! INFO @ Sat, 24 Aug 2019 21:59:18: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:59:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:59:19: #2 number of paired peaks: 69 WARNING @ Sat, 24 Aug 2019 21:59:19: Too few paired peaks (69) 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 21:59:19: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5820057/SRX5820057.10_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/SRX5820057/SRX5820057.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5820057/SRX5820057.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5820057/SRX5820057.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換中... INFO @ Sat, 24 Aug 2019 21:59:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5820057/SRX5820057.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5820057/SRX5820057.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5820057/SRX5820057.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5820057/SRX5820057.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 21:59:26: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:59:26: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:59:32: 1000000 INFO @ Sat, 24 Aug 2019 21:59:38: 2000000 INFO @ Sat, 24 Aug 2019 21:59:44: 3000000 INFO @ Sat, 24 Aug 2019 21:59:49: #1 tag size is determined as 45 bps INFO @ Sat, 24 Aug 2019 21:59:49: #1 tag size = 45 INFO @ Sat, 24 Aug 2019 21:59:49: #1 total tags in treatment: 436068 INFO @ Sat, 24 Aug 2019 21:59:49: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:59:49: #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 21:59:49: #1 tags after filtering in treatment: 413584 INFO @ Sat, 24 Aug 2019 21:59:49: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 24 Aug 2019 21:59:49: #1 finished! INFO @ Sat, 24 Aug 2019 21:59:49: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:59:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:59:49: #2 number of paired peaks: 69 WARNING @ Sat, 24 Aug 2019 21:59:49: Too few paired peaks (69) 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 21:59:49: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5820057/SRX5820057.20_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/SRX5820057/SRX5820057.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5820057/SRX5820057.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5820057/SRX5820057.20_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。