FAQ / Troubleshooting

MAFFT failed (return code 1) on Windows

Most often this happens when:

You copied only mafft.bat but not the full MAFFT distribution folder, or
The GUI/runner is pointing to the wrong file.

Fix:

Use the full MAFFT Windows distribution folder.
Point the pipeline to the launcher (often mafft.bat) in the GUI Advanced panel or via --mafft.

BLAST table is missing

The pipeline will only write *_blast.tsv if:

blastn is discoverable, and
the database prefix points to a formatted nucleotide database

Double-check:

blast/HmtG_database_PacBio.nsq (and siblings) exist
You are using the prefix (no file extension)

The PDF report is missing a figure

Common causes:

matplotlib or Pillow is missing
Matplotlib backend issues on some systems (e.g., headless runs)

Fix:

Ensure dependencies are installed (pip install matplotlib pillow)
Try setting a headless-safe backend before running:
- Linux/macOS:
```
export MPLBACKEND=Agg
```
- Windows (CMD):
```
set MPLBACKEND=Agg
```

Where are my intermediate files?

By design, the pipeline writes intermediate files alongside final outputs using the same prefix. These include the subsample FASTQ/FASTA and the raw MAFFT alignment.

If you are using a GUI wrapper that creates timestamped run folders, check inside the run folder.