Problems with Exonerate output

Question

[lumramabaja]

I am a first year bioinformatics bachelor student and I am using exonerate for the first time, however I am facing some difficulties with its output. All I am receiving is "-- completed exonerate analysis", without any error.

The code I am using is:

exonerate --model protein2genome --showalignment \
--query protein.fasta \
--target genome.fasta

Can anybody inform me how to get the actual output?

[helloword]

Hi, I am facing the exact issue. It has been 6.8 years but how did you fix this? Thanks in advance.

Answer 1

[zoo741]

You can get the output by adding >output.file.name to your command.

Answer 2

[Prakki Rama]

Try this:

exonerate --model protein2genome queryProtein.fasta Genome.fasta --showcigar no --showvulgar no --bestn 1 --showquerygff no >>output.e2g.out

[helloword]

Hi! I know it has been a long time but I cannot solve this issue. If you remember how to solve it, could you please help me? Compiling it as you suggest did not work.

[Prakki Rama]

Hi. So sorry. I have not used exonerate for so many years and I am currently not able to invest time on this. Please post your error as a new question, hopefully, some forum member will help resolve your issue.