Job ID = 2008176 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,398,458 reads read : 6,796,916 reads written : 6,796,916 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR629049.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: 00:10:24 3398458 reads; of these: 3398458 (100.00%) were paired; of these: 744682 (21.91%) aligned concordantly 0 times 2345034 (69.00%) aligned concordantly exactly 1 time 308742 (9.08%) aligned concordantly >1 times ---- 744682 pairs aligned concordantly 0 times; of these: 192219 (25.81%) aligned discordantly 1 time ---- 552463 pairs aligned 0 times concordantly or discordantly; of these: 1104926 mates make up the pairs; of these: 990280 (89.62%) aligned 0 times 50305 (4.55%) aligned exactly 1 time 64341 (5.82%) aligned >1 times 85.43% overall alignment rate Time searching: 00:10:24 Overall time: 00:10:24 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] 366702 / 2831644 = 0.1295 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 17:47:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585712/ERX585712.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585712/ERX585712.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585712/ERX585712.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585712/ERX585712.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 17:47:45: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:47:45: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:47:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585712/ERX585712.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585712/ERX585712.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585712/ERX585712.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585712/ERX585712.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 17:47:46: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:47:46: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:47:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585712/ERX585712.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585712/ERX585712.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585712/ERX585712.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585712/ERX585712.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 17:47:46: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:47:46: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:47:55: 1000000 INFO @ Fri, 05 Jul 2019 17:47:57: 1000000 INFO @ Fri, 05 Jul 2019 17:47:59: 1000000 INFO @ Fri, 05 Jul 2019 17:48:05: 2000000 INFO @ Fri, 05 Jul 2019 17:48:07: 2000000 INFO @ Fri, 05 Jul 2019 17:48:13: 2000000 INFO @ Fri, 05 Jul 2019 17:48:15: 3000000 INFO @ Fri, 05 Jul 2019 17:48:17: 3000000 INFO @ Fri, 05 Jul 2019 17:48:25: 4000000 INFO @ Fri, 05 Jul 2019 17:48:27: 3000000 INFO @ Fri, 05 Jul 2019 17:48:27: 4000000 INFO @ Fri, 05 Jul 2019 17:48:34: 5000000 INFO @ Fri, 05 Jul 2019 17:48:35: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 17:48:35: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 17:48:35: #1 total tags in treatment: 2296711 INFO @ Fri, 05 Jul 2019 17:48:35: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:48:35: #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 17:48:35: #1 tags after filtering in treatment: 1625062 INFO @ Fri, 05 Jul 2019 17:48:35: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 05 Jul 2019 17:48:35: #1 finished! INFO @ Fri, 05 Jul 2019 17:48:35: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:48:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:48:35: #2 number of paired peaks: 20 WARNING @ Fri, 05 Jul 2019 17:48:35: Too few paired peaks (20) 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 @ Fri, 05 Jul 2019 17:48:35: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX585712/ERX585712.10_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/ERX585712/ERX585712.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585712/ERX585712.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585712/ERX585712.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:48:37: 5000000 INFO @ Fri, 05 Jul 2019 17:48:38: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 17:48:38: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 17:48:38: #1 total tags in treatment: 2296711 INFO @ Fri, 05 Jul 2019 17:48:38: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:48:38: #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 17:48:38: #1 tags after filtering in treatment: 1625062 INFO @ Fri, 05 Jul 2019 17:48:38: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 05 Jul 2019 17:48:38: #1 finished! INFO @ Fri, 05 Jul 2019 17:48:38: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:48:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:48:38: #2 number of paired peaks: 20 WARNING @ Fri, 05 Jul 2019 17:48:38: Too few paired peaks (20) 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 @ Fri, 05 Jul 2019 17:48:38: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX585712/ERX585712.20_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/ERX585712/ERX585712.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585712/ERX585712.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585712/ERX585712.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:48:40: 4000000 INFO @ Fri, 05 Jul 2019 17:48:53: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 17:48:54: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 17:48:54: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 17:48:54: #1 total tags in treatment: 2296711 INFO @ Fri, 05 Jul 2019 17:48:54: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:48:54: #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 17:48:54: #1 tags after filtering in treatment: 1625062 INFO @ Fri, 05 Jul 2019 17:48:54: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 05 Jul 2019 17:48:54: #1 finished! INFO @ Fri, 05 Jul 2019 17:48:54: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:48:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:48:54: #2 number of paired peaks: 20 WARNING @ Fri, 05 Jul 2019 17:48:54: Too few paired peaks (20) 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 @ Fri, 05 Jul 2019 17:48:54: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX585712/ERX585712.05_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/ERX585712/ERX585712.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585712/ERX585712.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585712/ERX585712.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。