batchfile

Input of place_batch: a tab-separated file with three columns and no header.

Column	Content
1	Query alignment (FASTA, aligned to the reference package’s alignment).
2	Reference package directory (contains CONTENTS.json).
3	Output jplace file.

Rows sharing a reference package are placed together. Query names must be unique within each reference package. Empty lines and lines starting with # are ignored.

Example

runs/part00/tree_2/user_msa_file.fasta      pplacer/gtdbtk.package.2.refpkg runs/part00/tree_2/pplacer.class_level.bac120.json
runs/part01/tree_2/user_msa_file.fasta      pplacer/gtdbtk.package.2.refpkg runs/part01/tree_2/pplacer.class_level.bac120.json
runs/part00/tree_8/user_msa_file.fasta      pplacer/gtdbtk.package.8.refpkg runs/part00/tree_8/pplacer.class_level.bac120.json