MAKER2 no FASTAs generated

Question

[jamie.pike]

I have recently used MAKER2 for genome annotation. The run appears to have been successful, but when I came to use fasta_merge -d there was no output! gff3_merge -d worked fine, producing a new file AGND01.1.all.gff. I decided to check if any FASTAs had been generated using find . -type f -name "*.fa" in the AGND01.1_datastore directory generated by MAKER, but there were no results. Does this mean that MAKER did not produce and FASTAs for the contigs it annotated? If so, how do I fix this? Is there an option I must choose in the .ctl files?

Thanks,

Jamie

[lieven.sterck]

is your find cmdline accurate enough? I mean it's not the fasta files are called .FA or .fasta or such ('cus then your find will not report them)

[jamie.pike]

Ah, that seems obvious now you say it!! I have just tried find . -type f -name "*.fasta" which has produced results. It still does not explain why fasta_merge -d AGND01.1_master_datastore_index.log is not working though. Would you perhaps know why?

[lieven.sterck]

no it does not indeed :)

no errors/warnings or such, I assume?

[jamie.pike]

Nope, no errors or warning at all. I have had a look at where the fastas are and they are in a subdirectory e.g. AGND01.1.maker.output/AGND01.1_datastore/1D/3B/AGND01000482.1/theVoid.AGND01000482.1/query.fasta

not where the gff outputs are e.g.

AGND01.1.maker.output/AGND01.1_datastore/1D/3B/AGND01000482.1/AGND01000482%2E1.gff

So I am still wondering if MAKER generated the correct fastas?

Answer 1

[Kinoppy]

Hi Jamie, I have also encountered the same issue. Were you by any chance able to find a solution or understand why MAKER was giving that error?

Thank you