Job ID = 2641229 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 12,247,252 reads read : 24,494,504 reads written : 24,494,504 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: 00:03:21 12247252 reads; of these: 12247252 (100.00%) were paired; of these: 11746685 (95.91%) aligned concordantly 0 times 455203 (3.72%) aligned concordantly exactly 1 time 45364 (0.37%) aligned concordantly >1 times ---- 11746685 pairs aligned concordantly 0 times; of these: 515785 (4.39%) aligned discordantly 1 time ---- 11230900 pairs aligned 0 times concordantly or discordantly; of these: 22461800 mates make up the pairs; of these: 18881010 (84.06%) aligned 0 times 3224021 (14.35%) aligned exactly 1 time 356769 (1.59%) aligned >1 times 22.92% overall alignment rate Time searching: 00:03:21 Overall time: 00:03:21 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] 688295 / 1012526 = 0.6798 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:12:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5820063/SRX5820063.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5820063/SRX5820063.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5820063/SRX5820063.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5820063/SRX5820063.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 22:12:42: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:12:42: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:12:48: 1000000 INFO @ Sat, 24 Aug 2019 22:12:54: 2000000 INFO @ Sat, 24 Aug 2019 22:13:01: 3000000 INFO @ Sat, 24 Aug 2019 22:13:08: 4000000 INFO @ Sat, 24 Aug 2019 22:13:09: #1 tag size is determined as 45 bps INFO @ Sat, 24 Aug 2019 22:13:09: #1 tag size = 45 INFO @ Sat, 24 Aug 2019 22:13:09: #1 total tags in treatment: 265835 INFO @ Sat, 24 Aug 2019 22:13:09: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:13:09: #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 22:13:09: #1 tags after filtering in treatment: 249059 INFO @ Sat, 24 Aug 2019 22:13:09: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 24 Aug 2019 22:13:09: #1 finished! INFO @ Sat, 24 Aug 2019 22:13:09: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:13:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:13:09: #2 number of paired peaks: 71 WARNING @ Sat, 24 Aug 2019 22:13:09: Too few paired peaks (71) 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 22:13:09: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5820063/SRX5820063.05_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/SRX5820063/SRX5820063.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5820063/SRX5820063.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5820063/SRX5820063.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:13:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5820063/SRX5820063.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5820063/SRX5820063.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5820063/SRX5820063.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5820063/SRX5820063.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 22:13:12: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:13:12: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:13:18: 1000000 INFO @ Sat, 24 Aug 2019 22:13:24: 2000000 INFO @ Sat, 24 Aug 2019 22:13:31: 3000000 INFO @ Sat, 24 Aug 2019 22:13:38: 4000000 INFO @ Sat, 24 Aug 2019 22:13:39: #1 tag size is determined as 45 bps INFO @ Sat, 24 Aug 2019 22:13:39: #1 tag size = 45 INFO @ Sat, 24 Aug 2019 22:13:39: #1 total tags in treatment: 265835 INFO @ Sat, 24 Aug 2019 22:13:39: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:13:39: #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 22:13:39: #1 tags after filtering in treatment: 249059 INFO @ Sat, 24 Aug 2019 22:13:39: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 24 Aug 2019 22:13:39: #1 finished! INFO @ Sat, 24 Aug 2019 22:13:39: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:13:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:13:39: #2 number of paired peaks: 71 WARNING @ Sat, 24 Aug 2019 22:13:39: Too few paired peaks (71) 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 22:13:39: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5820063/SRX5820063.10_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/SRX5820063/SRX5820063.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5820063/SRX5820063.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5820063/SRX5820063.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:13:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5820063/SRX5820063.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5820063/SRX5820063.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5820063/SRX5820063.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5820063/SRX5820063.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 22:13:42: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:13:42: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:13:48: 1000000 INFO @ Sat, 24 Aug 2019 22:13:54: 2000000 INFO @ Sat, 24 Aug 2019 22:14:01: 3000000 INFO @ Sat, 24 Aug 2019 22:14:08: 4000000 INFO @ Sat, 24 Aug 2019 22:14:09: #1 tag size is determined as 45 bps INFO @ Sat, 24 Aug 2019 22:14:09: #1 tag size = 45 INFO @ Sat, 24 Aug 2019 22:14:09: #1 total tags in treatment: 265835 INFO @ Sat, 24 Aug 2019 22:14:09: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:14:09: #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 22:14:09: #1 tags after filtering in treatment: 249059 INFO @ Sat, 24 Aug 2019 22:14:09: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 24 Aug 2019 22:14:09: #1 finished! INFO @ Sat, 24 Aug 2019 22:14:09: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:14:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:14:09: #2 number of paired peaks: 71 WARNING @ Sat, 24 Aug 2019 22:14:09: Too few paired peaks (71) 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 22:14:09: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5820063/SRX5820063.20_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/SRX5820063/SRX5820063.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5820063/SRX5820063.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5820063/SRX5820063.20_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。