I am running a BLASTN of about 150 sequences against a genome that is 2.2 gigabases long. A few of my queries are actually full length BAC end sequences running to around 150,000 bases. I expect to find huge, contiguous hits for some BACs in the genome. Here's the command I use -
blastn 80BACs.fasta -db mygenome -out 80BACsBLAST -outfmt 10 -num_threads 8 -evalue 10e-3 -index_name mygenomeMBI
Around 10 minutes after it starts running, the program halts after producing a segmentation fault. I did a 'ulimit -s unlimited' to set the stack size to unlimited, but to no avail. I also went easy on the number of threads in subsequent trials, setting num_threads to 5 and subsequently, 2 - but that didn't help either.
I am using the binaries from rmblast-1.2-ncbi-blast-2.2.23+. I had earlier run a smaller query dataset against the same genome which worked fine, the BLAST completed in half a day. This issue, I am convinced is most definitely due to some very very long query sequences - I'd highly appreciate any help in this regard!