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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

File:CLCAssemblyAll454HvCatIllumRepBaseFungi.fasta.tbl