freebayes not reading the chunks of regions file

Question

[evafinegan]

Hello,

I am using freebayes for SNP calling using:

RUN=${SLURM_ARRAY_TASK_ID}
INPUT_DIR=/path/
OUTPUT_DIR=/path/
INPUT=$(ls $INPUT_DIR/*.txt | sed -n ${RUN}p)
SAMPLE=$(basename "$INPUT" .txt)

freebayes  -f genome.fasta \
          -L list_of_bam.txt \
          --targets  ${INPUT_DIR}/myfile${RUN}.txt > ${OUTPUT_DIR}/${SAMPLE}_.vcf

However, it gives error:

RUN #1 with sample myfile00
bed targets file is not open

I think it is not reading the subset files (total 50) that I made using split. Can you please help me figure out what is my mistake in the array. Thank you!

[Andrés Ribone]

Where are you specifying the region?