Tblastn Vdb

# 1) Search unaligned reads only with tabular output
tblastn_vdb \
  -query proteins.fa \
  -db SRR123456 \
  -sra_mode 0 \
  -outfmt 6 \
  -evalue 1e-6 \
  -num_threads 8

# 2) Search aligned reference sequences only
tblastn_vdb \
  -query proteins.fa \
  -db SRR123456 \
  -sra_mode 1 \
  -out aligned_refs.txt

# 3) Include filtered reads and search from a PSI-BLAST checkpoint
tblastn_vdb \
  -in_pssm profile.chk \
  -db SRR123456 \
  -sra_mode 2 \
  -include_filtered_reads \
  -outfmt "6 qaccver saccver pident length evalue bitscore"

Recommended Workflow

1. Confirm the target is an SRA or WGS-backed VDB source and not an ordinary local BLAST database.
2. Decide whether you want unaligned reads, aligned reference sequences, or both, then set -sra_mode explicitly.
3. Choose reproducible search settings up front: -outfmt, -evalue, -matrix, -comp_based_stats, and -num_threads.
4. Start with a small query or accession subset before scaling the search across larger read-backed databases.

Guardrails

• -db here means an SRA or WGS database name; it is not a standard local BLAST DB path.
• This build uses BLAST+ single-dash conventions such as -help and -version; autogenerated --help or --version captures are wrong for the live binary.
• Bare invocation fails with Must specify at least one SRA/WGS database, so missing -db is the first thing to check.
• -sra_mode 0 searches unaligned reads only, 1 searches aligned reference sequences only, and 2 searches both; record that choice in reproducible workflows.
• -query and -in_pssm are mutually exclusive, and -db_gencode matters if the subject database needs a non-standard translation table.