GUNC diamond output filename

[jsgounot]

Hi,

for some samples I had this error:

...
15:45:52 : No genes mapped to reference: SemiBin_95
15:45:52 : No genes mapped to reference: SemiBin_96
15:45:52 : No genes mapped to reference: SemiBin_97
15:45:52 : No genes mapped to reference: SemiBin_98
15:45:52 : No genes mapped to reference: SemiBin_99
15:45:52 : No genes mapped to reference: SemiBin_9
15:45:52 : No diamond output files.

When I list my diamond output files:

SemiBin_101.diamond.out
SemiBin_100.diamond.out
SemiBin_1005.diamond.out
SemiBin_1004.diamond.out
SemiBin_0.diamond.out
...
SemiBin_101.diamond.progenomes_2.1.out
SemiBin_100.diamond.progenomes_2.1.out
SemiBin_1005.diamond.progenomes_2.1.out
SemiBin_1004.diamond.progenomes_2.1.out
SemiBin_0.diamond.progenomes_2.1.out

I checked the source code, and the issue looks like to be triggered here:

gunc/gunc/gunc.py

Line 732 in 0e64c39

diamond_outdir, "diamond_output", f"{basename}.diamond.out"

that I guess should be changed (in my case) to:

diamond_outdir, "diamond_output", f"{basename}.diamond.progenomes_2.1.out"

that is only triggered when there is one diamond output file missing

gunc/gunc/gunc.py

Line 693 in 0e64c39

if not args.gene_calls and len(diamond_outfiles) != len(fastas):

I don't know if this is a bug. Maybe the database name changed, modifying the output name? Not sure.

[jsgounot]

Small edit:

gunc/gunc/gunc.py

Line 485 in 0e64c39

outfile = os.path.join(out_dir, f"{os.path.basename(infile)}.diamond.{db}.out")

Looks like a bug :)
Need to add the db name in the add_empty_diamond_output function.