Troubleshooting

Host indexes rebuild unexpectedly

Host Bowtie indexes are reused only when the expected .ebwt or .ebwtl files already exist next to the original host FASTA files.

GitHub SSH push fails

Use the working SSH key explicitly when needed:

GIT_SSH_COMMAND='ssh -i ~/.ssh/aion -o IdentitiesOnly=yes' git push

Resume does not skip a stage

A stage is skipped only if: - the completion marker exists - the expected output files for that stage exist

Assembly or novel steps fail immediately

Check that both sample-specific paths are present: - assembly_fasta - assembly_gff