#!/bin/bash
while IFS= read -r line; do
    assem=${line}_df38
    echo Prepping $assem
    # test if directory is empty
    /bin/time /home/agray/te_idx/target/release/te_idx --assembly $assem prepare-assembly &> "/usr/local/Dfam-warehouse/releases/annotations_exports/_logs/${assem}_index.log"

done < "$1"