Does the "run_pipeline.sh" script ignore "Run modeling w/ trRefine output" part automatically?

[EstherBear]

The "Run trRefine" part creates a file named DONE_iter1 which make "! -f $WDIR/DONE_iter1" false.

############################################################
# 7. Run trRefine
############################################################
if [ ! -s $WDIR/t000_.trRefine.npz ]
then
    echo "Running trRefine"
    cd $WDIR
    python $PIPEDIR/trRefine/run_trRefine_DAN.py -msa_npz $WDIR/t000_.msa.npz \
        -tbm_npz $WDIR/t000_.tbm.npz -pdb_dir_s $WDIR/pdb-msa $WDIR/pdb-tbm \
        -a3m_fn $WDIR/t000_.msa0.a3m -hhr_fn $WDIR/t000_.hhr\
        -n_core $CPU > $WDIR/log/trRefine.stdout 2> $WDIR/log/trRefine.stderr
    cd ..
    touch $WDIR/DONE_iter1
fi

############################################################
# 8. Run modeling w/ trRefine output
############################################################

if [ ! -f $WDIR/DONE_iter1 ]

[gjoni]

That's a bug - thanks for catching it! touch $WDIR/DONE_iter1 should not be there. Fixed now.