MetaPro v4.0.3: GA_BT2 uses Bowtie2 but downloaded family_group database contains only BWA indexes

[willem-stock]

Thank you for this great pipeline.

I'm running MetaPro v4.0.3 in an Apptainer container on an HPC (PBS scheduler) using paired-end Illumina metatranscriptomic data.

Metapro fails during the GA_BT2 stage because the generated jobs invoke Bowtie2 against reference databases that only contain BWA indexes.

The downloaded database contains:

family_group/
genus_group/
order_group/
choco_h3_family/
choco_h3_genus/
choco_h3_order/

The family_group directory contains FASTA files together with BWA index files:

XXXX.fasta
XXXX.fasta.amb
XXXX.fasta.ann
XXXX.fasta.bwt
XXXX.fasta.pac
XXXX.fasta.sa

The archived choco_h3_family.tar.gz also seems to contain BWA index files rather than Bowtie2 indexes.

Relevant settings within my config.ini:

source_taxa_db = /scratch/.../metapro_db/family_group
DNA_DB = /scratch/.../metapro_db/family_group
taxid_tree = /scratch/.../metapro_db/taxid_trees/family_tree.tsv #downloaded separately
kraken2_db = /scratch/.../metapro_db

The GA pre-scan completes successfully and produces a populated lib_list.txt.

The generated GA_BT2 job scripts seems to invoke Bowtie2:

bowtie2 \
    -x /scratch/.../metapro_db/family_group/2303507.fasta \
    -U .../s.fastq \
    | samtools view >> .../s.sam

However, that reference only has BWA indexes:

2303507.fasta
2303507.fasta.amb
2303507.fasta.ann
2303507.fasta.bwt
2303507.fasta.pac
2303507.fasta.sa

and therefore Bowtie2 exits with:

(ERR): ".../family_group/2303507.fasta" does not exist or is not a Bowtie 2 index
Exiting now ...

This occurs repeatedly for many taxon-specific databases.

Is this an incompatibility between the v4.0.3 container and the current downloadable database?

Specifically, should the family_group database now contain Bowtie2 (*.bt2) indexes instead of BWA indexes?
Or should the generated GA_BT2 jobs still be using BWA?

thank you for you time