My assembly has close to 10788231 contigs. Surprisingly prokka runs fine on truncated versions of the same assembly. Like, I tried running it on a truncated version of the same assembly with 1382450 contings and it ran like a charm. It would be great if I could get any help regarding this.
I have been constantly getting this error since the past 1 week, whenever I try to run prokka on my metagenome assembly
"Running: cat mydir1C_metagenome\/air.sprot.tmp.3054131.faa | parallel --gnu --plain -j 200 --block 1758462 --recstart '>' --pipe blastp -query - -db /nfs/home/adhar/anaconda3/db/kingdom/Bacteria/sprot -evalue 1e-09 -qcov_hsp_perc 80 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > mydir1C_metagenome\/air.sprot.tmp.3054131.blast 2> /dev/null [06:14:57] Could not run command: cat mydir1C_metagenome\/air.sprot.tmp.3054131.faa | parallel --gnu --plain -j 200 --block 1758462 --recstart '>' --pipe blastp -query - -db /nfs/home/adhar/anaconda3/db/kingdom/Bacteria/sprot -evalue 1e-09 -qcov_hsp_perc 80 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > mydir1C_metagenome\/air.sprot.tmp.3054131.blast 2> /dev/null"
My assembly has close to 10788231 contigs. Surprisingly prokka runs fine on truncated versions of the same assembly. Like, I tried running it on a truncated version of the same assembly with 1382450 contings and it ran like a charm. It would be great if I could get any help regarding this.
Thanks