SEPP hangs, and fails to finish or proceed on rare instances

[smirarab]

chdir to this directory
/scratch/cluster/namphuon/metagen/test2

Run this command to reproduce it:

/lusr/bin/python run_tipp.py -t
/projects/sate5/metagen/data/refpkg/rpsB.refpkg/sate.taxonomy -a
/projects/sate5/metagen/data/refpkg/rpsB.refpkg/sate.fasta -r
/projects/sate5/metagen/data/refpkg/rpsB.refpkg/sate.taxonomy.RAxML_info
-x 1 -at 0.95 -pt 0.95 -tx
/scratch/cluster/namphuon/metagen/refpkg/rpsB.refpkg/all_taxon.taxonomy
-txm /scratch/cluster/namphuon/metagen/refpkg/rpsB.refpkg/species.mapping
-adt /projects/sate5/metagen/data/genes/rpsB/results/RAXML_SATE/sate.tree.ml
-A 50 -d /scratch/cluster/namphuon/metagen/test2 -p
/scratch/cluster/namphuon/metagen/test2/temp -f
/projects/sate5/metagen/data/fragments4/rpsB.fas -c
/projects/sate5/metagen/scripts/configs/old.config -o
tipp.align_95_size_100.rpsB -cp
/scratch/cluster/namphuon/metagen/test2/checkpoint -cpi 600