I'm trying to get a webservice for protein discovery running. I would like to perform a tblastn with a PSSM from NCBI's archive (smp file). This works fine with NCBI BLAST+, but unfortunately the framework I should run it from only supports the old NCBI BLAST (2.2.21).
So I'm searching for a equivalent command to
tblastn -in_pssm matrix.smp -db database -evalue 1e-10 -out outfile -outfmt 6
and what I came up with was
blastall -p psitblastn -d database -R matrix.smp -o outfile -e 1e-10 -m 8
This command, however, has been running for hours without producing any output, error message, or consuming any cpu time (ps -A | grep blastall yields 0:00:00)
What am I doing wrong?