Frequently Asked Questions (FAQ)

My search is taking a long time. What can I do?

Most likely your search is returning a lot of results. The search commands have several options to reduce the number of results returned, such as --limit.

How can I run workflows with many structure files on an HPC filesystem?

If your cluster home/project filesystem is slow with many small files, run the high-file-count steps in local scratch and archive results to persistent storage. A common scratch policy is automatic cleanup of files older than 14 days, but this policy is cluster-specific.

Use the same commands from the README, but point temporary directories and cache to scratch:

SCRATCH_RUN="${SCRATCH:-/tmp}/${USER}/protein-quest-run"
PERSIST_DIR="$HOME/protein-quest-results"
mkdir -p "$SCRATCH_RUN/cache" "$PERSIST_DIR"

# Example: retrieve and filter on scratch (many files)
protein-quest retrieve alphafold \
    --cache-dir "$SCRATCH_RUN/cache" \
    alphafold.csv "$SCRATCH_RUN/downloads-af"

protein-quest filter confidence \
    --confidence-threshold 50 \
    --min-residues 100 \
    --max-residues 1000 \

    "$SCRATCH_RUN/downloads-af" "$SCRATCH_RUN/filtered"

# Bundle outputs for persistent storage (home/project)
tar -C "$SCRATCH_RUN" -cf "$PERSIST_DIR/filtered-$(date +%F).tar" filtered

To resume later, unpack the tarball again to scratch:

mkdir -p "$SCRATCH_RUN"
tar -C "$SCRATCH_RUN" -xf "$PERSIST_DIR/filtered-2026-02-27.tar"

This pattern keeps active runs fast on scratch while storing long-term results as a small number of tarballs in persistent storage.

If you have downstream tools that cannot read from tarballs, you can mount the tarball as a filesystem with ratarmount and unmount with fusermount -u <mount_point>.

My log is polluted with progress bar lines. How can I fix this?

To reduce the number of lines printed by the progress bar, you can increase the minimum interval between updates with the TQDM_MININTERVAL environment variable. For example, setting it to 9 will update the progress bar every 9 seconds instead of every 0.1 seconds.

To not have any progress bars at all, you can set TQDM_DISABLE environment variable to any value.

My protein-quest question is not answered here. Where can I get help?

Please see the Contributing document for instructions on how to ask questions and report issues.