View Masking CLC Assemblies
Masking Third Hybrid Assembly CLC
/opt/RepeatModeler/BuildDatabase -name ThirdHybridAssemblyCLC_RMOD.fasta /data/process/DBs/cenicafe/rust/genome/ThirdHybridAssemblyCLC.fasta
/opt/RepeatModeler/RepeatModeler -database ThirdHybridAssemblyCLC_RMOD.fasta > run.out
Concatenating Fungi repeat database + repBase output from Repeatmodeler
cat RM_3565.FriMar230955502012/consensi.fa.classified Fungi_n_ancestralrepeats.fasta > RepBase_Fungi_Roya.fasta
Run RepeatMasker
RepeatMasker -pa 4 -s -div 20 -no_is -nocut -lib RepBase_Fungi_Roya.fasta /data/process/DBs/cenicafe/rust/genome/ThirdHybridAssemblyCLC.fasta
File:ThirdHybridAssemblyCLC.fasta.tbl
Masking CLCAssemblyAll454HvCatIllum
/data/process/Roya/maskedCLCAssemblyAll454HvCatIllum$ /opt/RepeatModeler/BuildDatabase -name CLCAssemblyAll454HvCatIllum_RMOD.fasta CLCAssemblyAll454HvCatIllum.fasta
/opt/RepeatModeler/RepeatModeler -database CLCAssemblyAll454HvCatIllum_RMOD.fasta > run.out
Program duration is 1814.0 sec = 30.2 min = 0.5 hr
sh: Syntax error: Bad fd number
sh: Syntax error: Bad fd number
sh: Syntax error: Bad fd number
eleredef failed. Exit code 8
Like can’t build own repeat database for this assembly, run repeatmasker with RepBase_Fungi_Roya.fasta
RepeatMasker -pa 4 -s div20 -no_is -nocut -lib /data/process/Roya/maskedAssemblies/RepBase_Fungi_Roya.fasta CLCAssemblyAll454HvCatIllum.fasta
File:CLCAssemblyAll454HvCatIllumRepBaseFungi Roya.fasta.tbl
RepeatMasker -pa 4 -s div20 -no_is -nocut -lib /data/process/Roya/maskedAssemblies/Fungi_n_ancestralrepeats.fasta CLCAssemblyAll454HvCatIllum.fasta