Optional analyses¶

The core workflow runs on CPUs. Frameshift screening uses the standard environment; the other optional analyses need separate tools or data.

Frameshift screening¶

This screen can recover viral marker domains that protein prediction misses. Enable it with --frameshift-screening. See the frameshift screening guide for an example and the method's limits.

Masking and taxonomy models¶

Install pixi install --locked -e optional and run ViroSync with pixi run -e optional virosync when enabling these analyses. Masking requires --no-skip-masking and exactly one execution.masking.repeatmasker_species or repeatmasker_library setting. For taxonomy models, set phase2.taxonomy_ml_enabled: true and choose phase2.taxonomy_ml_model: logreg, gbdt or xgboost. These analyses are off by default. Taxonomy ML supplies per-gene support to the outward extension controller. It cannot replace the confirmed seed, cross a host stop or move a boundary to isolated positive genes in a distant flank. If model fitting fails, extension uses the same deterministic evidence path as a run with taxonomy ML disabled.

TMVec2¶

TMVec2 adds BFVD protein-embedding evidence. It can use a CPU; a GPU is optional.

pixi install --locked -e structural
pixi run virosync orchestrate setup \
  --config config/orchestration.yaml \
  --no-write-config \
  --tmvec
pixi run -e structural check-structural-runtime --require-tmvec
pixi run -e structural virosync \
  -i genome.fna -o results/tmvec \
  --config config/orchestration.yaml \
  --device cpu --tmvec

For a GPU, replace --device cpu with --device cuda --tmvec-gpu. An enabled TMVec2 run stops if its runtime or resources fail validation. To check CUDA with check-structural-runtime, first set compute.device: cuda in the config.

Boltz and Foldseek¶

Install the structural environment and isolated Boltz runtime:

pixi install --locked -e structural
pixi install --locked --manifest-path tools/boltz_runtime/pixi.toml

Set the Foldseek database prefix and MSA-server mode in the config:

phase3:
  viral_structure_db: /data/viral_structures/db
  boltz_use_msa_server: true

This sends query protein sequences to an online MSA service.

Check and run the analysis:

pixi run -e structural check-structural-runtime --require-boltz
pixi run -e structural virosync \
  -i genome.fna -o results/boltz \
  --config config/orchestration.yaml \
  --boltz

An MCP fold inferred without a query structure is not a confirmed 3D structure. Use the Boltz and Foldseek results when query-structure evidence is required. If the runtime or database is missing, ViroSync warns and skips this layer.

InterProScan¶

Set phase3.interproscan_dir to an InterProScan directory that contains an executable interproscan.sh. Then check and run the layer:

pixi run check-structural-runtime --require-interproscan
pixi run virosync \
  -i genome.fna -o results/interproscan \
  --config config/orchestration.yaml \
  --interproscan

If the runtime is missing, ViroSync warns and skips this layer.

Check all optional layers¶

pixi run -e structural check-structural-runtime --require-all-optional

This command checks configured tools and data. It does not install them.