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gtonkinhill / panaroo

An updated pipeline for pangenome investigation
MIT License
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Invalid file extension #295

Closed MHassanSaeed closed 2 months ago

MHassanSaeed commented 3 months ago

Hi, I am using the following command to run Panaroo and getting a file extension error. I annotate the genome using prokka. Besides that, I tried using the off file from NCBI but still got the error.

panaroo -i Ent-11.gff -o entomo-prokka -a core --core_threshold 0.90 --merge_paralogs --clean-mode strict --aligner mafft --remove-invalid-genes -t 40

Traceback (most recent call last):
  File "/usr/panaroo/bin/panaroo", line 10, in <module>
    sys.exit(main())
  File "/usr/envs/panaroo/lib/python3.9/site-packages/panaroo/__main__.py", line 328, in main
    files.append(create_temp_gff3(line[0], line[1], temp_dir))
  File "//usr/envs/panaroo/lib/python3.9/site-packages/panaroo/prokka.py", line 102, in create_temp_gff3
    raise RuntimeError(f"Invalid file extension! ({ext})")
RuntimeError: Invalid file extension! ()

Thank you.

gtonkinhill commented 3 months ago

Hi,

Panaroo requires multiple GFF files to build a pangenome. As you are supplying only one (Ent-11.gff), it is assuming the file should be a list of paths to other GFFs which is causing the error.