What does this error mean? Error: option '-r' specified multiple times

[blahah]

It means exactly what it says - that you specified the -r argument multiple times in the same command. Can you paste your command here?

[amabdelhaliem]

WOW that's really a quick response! this is the command causing the problem: ~/programs/transrate-1.0.0-linux-x86_64/transrate --assembly ~/db/Fo2-Fo3-deNovo/trinity_out_dir/Trinity.fasta --left left.fq --right right.fq -threads 30 --outfile Transrate_out

[amabdelhaliem]

thanks.

[blahah]

the problem is that you used only a single - before threads - it should be --threads. Arguments with a single - are treated as single-letters arguments, so it was interpreted as -t -h -r -e -a -d -s :)

The full command you want is...

~/programs/transrate-1.0.0-linux-x86_64/transrate --assembly ~/db/Fo2-Fo3-deNovo/trinity_out_dir/Trinity.fasta --left left.fq --right right.fq --threads 30 --outfile Transrate_out

[amabdelhaliem]

Loading assembly :) fantastic, you are right, thanks Richard.

[blahah]

great! enjoy transrate :)