Fix thread count argument to run_pyrodigal in pharokka.py

gbouras13 · Sep 14, 2023 · fc3ecf0 · fc3ecf0
1 parent 10c940e
commit fc3ecf0
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/bin/pharokka.py b/bin/pharokka.py
@@ -283,12 +283,12 @@ def main():
             run_phanotate(input_fasta, out_dir, logdir)
     elif gene_predictor == "prodigal":
         logger.info("Implementing Prodigal using Pyrodigal.")
-        run_pyrodigal(input_fasta, out_dir, args.meta, args.coding_table, args.threads)
+        run_pyrodigal(input_fasta, out_dir, args.meta, args.coding_table, int(args.threads))
     elif gene_predictor == "genbank":
         logger.info("Extracting CDS information from your genbank file.")
     elif gene_predictor == "prodigal-gv":
         logger.info("Implementing Prodigal-gv using Pyrodigal-gv.")
-        run_pyrodigal_gv(input_fasta, out_dir, args.threads)
+        run_pyrodigal_gv(input_fasta, out_dir, int(args.threads))
 
     # translate fastas (parse genbank)
     translate_fastas(out_dir, gene_predictor, args.coding_table, args.infile)