Blastdbcheck

blastdbcheck

Quick Start

• Command: blastdbcheck -db <dbname> -dbtype <prot|nucl> [options]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/blastdbcheck
• Full reference: See references/help.md

When To Use This Tool

• Validate a BLAST database before running expensive searches.
• Diagnose corruption, missing files, or inconsistent volumes in an existing BLAST DB.
• Audit a whole directory tree of databases with -dir and -recursive.
• Enforce metadata expectations such as taxonomy IDs with -must_have_taxids.

Common Patterns

# 1) Quick integrity check of one protein database
blastdbcheck \
  -db swissprot \
  -dbtype prot \
  -verbosity 2

# 2) Exhaustive validation of a critical nucleotide database
blastdbcheck \
  -db nt \
  -dbtype nucl \
  -full \
  -verbosity 3

# 3) Sweep a directory of databases recursively
blastdbcheck \
  -dir /data/blastdb \
  -recursive \
  -verbosity 1

Recommended Workflow

1. Decide whether you are checking one database (-db) or scanning a directory (-dir).
2. Set -dbtype explicitly when the database name is ambiguous instead of relying on guess.
3. Start with the default summary mode, then escalate to -full, -random, -stride, or -ends depending on how much confidence you need.
4. Treat any failures as a database maintenance problem and repair or re-download the BLAST DB before running downstream searches.

Guardrails

• Use BLAST+ style flags such as -help and -version; the common GNU-style --help pattern is wrong here.
• -db is incompatible with -dir and -recursive.
• -full is incompatible with sampling modes such as -stride, -random, and -ends.
• -must_have_taxids is a policy check, not a repair step; older or custom databases may fail it legitimately.
• -cdd_delta is only meaningful for CDD / DELTA-BLAST related databases.