The command line for testing rnammer that is given in the doc is throwing an error when I execute it (CentOS 7):
../rnammer -S bac -m lsu,ssu,tsu -xml ecoli.xml -gff ecoli.gff -h ecoli.hmmreport < ecoli.fsa
Use of uninitialized value $fsa in string ne at ../rnammer line 265.
The command line for testing rnammer that is given in the doc is throwing an error when I execute it (CentOS 7): ../rnammer -S bac -m lsu,ssu,tsu -xml ecoli.xml -gff ecoli.gff -h ecoli.hmmreport < ecoli.fsa Use of uninitialized value $fsa in string ne at ../rnammer line 265.
However this worked: ../rnammer -S bac -m lsu,ssu,tsu -xml ecoli.xml -gff ecoli.gff -h ecoli.hmmreport -f ecoli.fsa
the files ecoli.xml, ecoli.gff, and ecoli.hmmreport are created and look OK, but the job hangs and I had to ctrl-C to exit the command.