We are trying to get the hang of a small cluster we just built. A co-worker launched a 10K query against the whole human genome. It has been running for 3 days now! He had previously launched a 1K query which took about 1hr. We are trying to understand what might have happened when we scaled up. Is a 10K query really that unreasonable or is something else likely to be going on. Is there anyway to check on exactly how much of a Blast job has been completed. Process currently running on 6 compute nodes, 4 are dual processor boards. Most have have 2G or more of memory. A quick look of the stats showed no more than 12% of available memory being used, less on most machines. Essentially no swap has been used to the best of my knowledge. We used the following syntax to launch the job: P4_GLOBMEMSIZE=268435456 time /opt/mpich/gnu/bin/mpirun -np 14 /usr/local/bin/mpiblast -p blastn -d whole_genome.fa -i /home/kieran/rnd.seq Thanks Paul