BUSCO gff file(s) not captured in output when Augustus used, no errors as stderr suppressed

[Hymenium]

Despite >90% of BUSCOs being matched in a genome, the buso_output.gff file is empty.

I'm not sure why this cat command doesn't get the contents of the .gff files. The path looks fine and the run_*/busco_sequences folder seems to be there, but error messages are redirected.

tools-iuc/tools/busco/busco.xml

Line 86 in bc94851

cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

It seems that it works when MetaEuk is selected but not Augustus.

I can't submit a bug report but here is a history demonstrating the issue on some tutorial data: https://usegalaxy.eu/u/hymenium/h/busco-gff-test

[igormakunin2]

We observed a similar issue, an empty gff file from Busco Galaxy Version 5.7.1+galaxy0, on Galaxy Australia. Busco. An early version of Busco, Galaxy Version 5.5.0+galaxy0, produces a valid (non-empty) gff file on the same nucleotide sequences. Both versions produce an empty gff file on protein sequences, but I don't know if gff output supported for protein inputs.