I ran the Spades software (https://github.com/ablab/spades), which outputs contigs.fasta

for f in `ls -1 *_1.fq | sed 's/_1.fq//’`;
    do spades.py -o . --mismatch-correction -1 $f\_1.fq -2 $f\_2.fq -t 20;
done

Within the same directory, I created and executed a bash script filter_contigs.sh:

for file in contigs.fasta; do
        grep -F ">" $file | sed -e 's/_/ /g' |sort -nrk 6 |awk '$6>=2.0 && $4>=500 {print $0}'|
        sed -e 's/ /_/g'|sed -e 's/>//g'>$file.txt
        echo sequences to keep
        wc -l $file.txt
        echo running fastagrep.pl
        ../fastagrep.pl -f $file.txt $file > HCov.$file
        echo sequences kept
        grep -c ">" HCov.$file
done

When I executed filter_contigs.sh, it fails to capture/keep any contigs. Why?

sequences to keep
0 contigs.fasta.txt
running fastagrep.pl
sequences kept
0