Not enough GFF files are provided. Some results might be omitted Error: gff2db failed

[abrozzi]

Expected Behavior

No error.

Current Behavior

Not enough GFF files are provided. Some results might be omitted
tmpFolder/15806226240676100088/createsetdb.sh: line 130:  9468 Segmentation fault      "${MMSEQS}" gff2db "${@}" "${TMP_PATH}/seqDB" "${OUTDB}_nucl" ${GFF2DB_PAR}
Error: gff2db failed

Steps to Reproduce (for bugs)

I downloaded 66 genomes (assemblies) from NCBI in fasta format:

conda activate ncbi_datasets
datasets download genome accession GCA_019927265.1 GCA_019927285.1 GCA_019927305.1 GCA_019927315.1  GCA_019927325.1 GCA_019927345.1 GCA_019927385.1 GCA_019927405.1  GCA_019927425.1 GCA_019927435.1 GCA_019927465.1 GCA_019927485.1GCA_019927505.1 GCA_019927525.1 GCA_019927535.1 GCA_019927565.1 GCA_019927585.1 GCA_019927605.1 GCA_019927625.1 GCA_019927645.1GCA_019927655.1 GCA_019927685.1 GCA_019927705.1 GCA_019927725.1GCA_019927745.1 GCA_019927765.1 GCA_019927785.1 GCA_019927805.1GCA_019927825.1 GCA_019927845.1 GCA_019927855.1 GCA_019927885.1GCA_019927905.1 GCA_019927925.1 GCA_019927945.1 GCA_019927965.1GCA_019927985.1 GCA_019928005.1 GCA_019928025.1 GCA_019928045.1GCA_019928065.1 GCA_019928075.1 GCA_019928105.1 GCA_019928115.1GCA_019928145.1 GCA_019928165.1 GCA_019928185.1 GCA_019928205.1GCA_019928215.1 GCA_019928245.1 GCA_019928265.1 GCA_019928285.1GCA_019928305.1 GCA_019928325.1 GCA_019928345.1 GCA_019928365.1GCA_019928385.1 GCA_019928395.1 GCA_019928405.1 GCA_019928445.1GCA_019928465.1 GCA_019928485.1 GCA_019928505.1 GCA_019928525.1GCA_019928545.1 GCA_019928565.1

For each one of them I ran:

prodigal -i ASM1992728v1.fna -o ASM1992728v1.gff -a ASM1992728v1.faa -f gff

and created the gffDir.txt

find "$(pwd)" -name "*.gff" > gffDir.txt

then I ran:

spacedust createsetdb ./*.fna setDB tmpFolder --gff-dir gffDir.txt --gff-type CDS

and get the error:

Not enough GFF files are provided. Some results might be omitted
tmpFolder/15806226240676100088/createsetdb.sh: line 130:  9468 Segmentation fault      "${MMSEQS}" gff2db "${@}" "${TMP_PATH}/seqDB" "${OUTDB}_nucl" ${GFF2DB_PAR}
Error: gff2db failed

[RuoshiZhang]

Hi! Sorry for the delay.
I have found the bug in gff2db, but it might take a bit of time to get it fixed, because this module is under MMseqs2.
I will post it here when there is a updated fix.
Alternatively, you could directly give the prodigal .faa files as the input.