hts_SuperDeduper not functioning in a bash loop

[lsuttenfield]

I am running hts_SuperDeduper sequentially on different samples. There's a recurrent issue where it will successfully run the first sample but exit with this error message without proceeding to the next sample. This does not seem to be version specific (tried an older version and it was fine).
ERROR: There are not either 3 (SE, itab3), 4 (SE, itab with tags) 5 (PE, itab5), or 6 (PE, itab6), or 8 (PE, itab6 with tags) elements within a tab delimited file line run_dedup_v2.sh: line 81: one: command not found

samples_file="/path/to/samples"
reads_file="/path/to/readnames"

cat "$samples_file" | while read -r line; do

    patient=$(echo "$line" | cut -d , -f 1)
    sample1=$(echo "$line" | cut -d , -f 2)

    file1=$(grep "${sample1}_" "$reads_file" | grep "R1")
    file2=$(grep "${sample1}_" "$reads_file" | grep "R2")

    echo $patient ; echo $sample1
    
    if [ "$(ls -A ../combined_runs/all_patients/${patient}/dedup/${sample1}/)" ]; then
    	echo "Warning: ../combined_runs/all_patients/${patient}/dedup/${sample1}/* are already present"
    else
        echo "Running hts_SuperDeduper on ${sample1}!"
        hts_SuperDeduper -1 "$file1" -2 "$file2" -f ../combined_runs/all_patients/${patient}/dedup/${sample1}/${sample1}.dedup
    fi
done

I'm using htstream v1.3.3 currently; I was using the current version earlier (downloaded with bioconda just a couple months ago).