error in sed usage

Question

[evafinegan]

Hello,

I am using this loop for a software"

RUN=$(printf "%02d" ${SLURM_ARRAY})
INPUT_DIR=/path
OUTPUT_DIR=/path
echo "RUN"
INPUT_FILE=$(ls $INPUT_DIR/*.bed | sed -n ${RUN}p)
SAMPLE=$(basename "$INPUT_FILE" .bed)
echo "RUN #${RUN} with sample ${SAMPLE}"
freebayes -f genome.fasta  \
          -L genome_1.txt \
          --targets ${INPUT_FILE}  > ${OUTPUT_DIR}/${SAMPLE}_.vcf

But I am getting error:

sed: -e expression #1, char 3: invalid usage of line address 0

Thank you for the help.

[JC]

what are you trying to do with sed? or what is the expected value of INPUT_FILE?

[evafinegan]

INPUT_FILE is expected to give each of the bed file name along with path to run with an array.

[JC]

I am not sure if freebayes --targets accepts more than one file, but in case you will need to put together in a single string, like:

INPUT_FILE=$(ls $INPUT_DIR/*.bed | perl -pe "s/\n/,/g")