Pipeline failed at prokka step

[manuss11]

Hello Dr Seemann,

I'm running Nullarbor and have the following error:

Running: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.13 from https://github.com/tseemann/prokka' -Z 4F\-69\/prokka\/contigs\.err -i 4F\-69\/prokka\/contigs\.fsa 2> /dev/null
[12:09:33] Could not run command: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.13 from https://github.com/tseemann/prokka' -Z 4F\-69\/prokka\/contigs\.err -i 4F\-69\/prokka\/contigs\.fsa 2> /dev/null
'4F-69/prokka/contigs.gff' -> '4F-69/contigs.gff'
cp: cannot stat '4F-69/prokka/contigs.gbk': No such file or directory
ln -f 6F-69/contigs.gff 6F-69.gff
ln -f O10-16/contigs.gff O10-16.gff
ln -f O7-16/contigs.gff O7-16.gff
ln -f O1-16/contigs.gff O1-16.gff
ln -f 15F-69/contigs.gff 15F-69.gff
ln -f O11-16/contigs.gff O11-16.gff
ln -f 13F-69/contigs.gff 13F-69.gff
ln -f 4F-69/contigs.gff 4F-69.gff
samtools faidx ref.fa
Could not build fai index ref.fa.fai
Makefile:133: recipe for target 'ref.fa.fai' failed
make: *** [ref.fa.fai] Error 1
make: Leaving directory '/home/qiime2/SERRATIAS19-2'

How could I solve it?

Thanks a lot

[tseemann]

This is a prokka error, not nullarbor. I thinl tbl2asn has expired (it expires every 6 months). You need to update it via your conda setup.