Troubleshooting

Common Issues and Fixes

Invalid node name

Symptom:

MirMachine prints an error panel saying the node is wrong.

Fix:

MirMachine.py --print-all-nodes

Then choose one of the listed nodes.

Genome file error

Symptom:

MirMachine reports that the genome file does not exist.

Fix:

• Verify the path passed to --genome.

• Use an uncompressed FASTA file.

Stalled Snakemake lock

Symptom:

Workflow stops because the working directory is locked.

Fix:

MirMachine.py --node Caenorhabditis --species run1 --genome genome.fa --unlock

Workflow cleanup

Delete generated outputs:

MirMachine.py --node Caenorhabditis --species run1 --genome genome.fa --remove

Mark targets as up to date:

MirMachine.py --node Caenorhabditis --species run1 --genome genome.fa --touch

Dry-run before execution:

MirMachine.py --node Caenorhabditis --species run1 --genome genome.fa --dry

Low-confidence or sparse predictions

• Verify that node and model are biologically appropriate.

• Try --model combined if families are missing in proto or deutero.

• Increase --evalue carefully to broaden inclusion (may increase low-quality hits).

Family not found in single-family mode

Use:

MirMachine.py --print-all-families

Then pick a family name shown in the output.