prokka issue with blast2- executing singularity

[anugos]

Hi I am running prokka on singularity using commands below. I have also called BLAST 2.12 still running through the error in CDS annotation. Appreciate your help.

Command used

$module load Nextflow $module load Singularity $module load BLAST/2.12.0-Linux_x86_64 $singularity build prokka.sif docker://staphb/prokka:latest $singularity exec prokka.sif prokka -h $singularity exec prokka.sif prokka group-10.contigs.fa --outdir results/prokka --force --norrna --notrna

Error

[11:00:53] There are still 1149143 unannotated CDS left (started with 1149143) [11:00:53] Will use blast to search against /prokka-1.14.5/db/kingdom/Bacteria/IS with 8 CPUs

Could not run command: cat results/prokka/PROKKA_06212022.IS.tmp.119347.faa | parallel --gnu --plain -j 8 --block 7738131 --recstart '>' --pipe blastp -query - -db /prokka-1.14.5/db/kingdom/Bacteria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > results/prokka/PROKKA_06212022.IS.tmp.119347.blast 2> /dev/null

Thanks. -Anu

[kapsakcj]

You can try running that last command in the output, without the 2> /dev/null in order to see the error message. I have a feeling the issue has to do with the temporary directory that's used when running prokka in the singularity container. Try this, pending you have all of your intermediate files from when you initally ran the prokka

cat results/prokka/PROKKA_06212022.IS.tmp.119347.faa | parallel --gnu --plain -j 8 --block 7738131 --recstart '>' --pipe blastp -query - -db /prokka-1.14.5/db/kingdom/Bacteria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > results/prokka/PROKKA_06212022.IS.tmp.119347.blast

You may want to also try using a directory in the singularity container that you have permissions to write in. I would suggest using /data inside the container and mount your PWD from your host computer to /data in the container. You could try this:

singularity exec -B $PWD:/data prokka.sif prokka /data/group-10.contigs.fa --outdir /data/results/prokka --force --norrna --notrna