VIBRANT not generating information in outfiles

Hi there,

I am having some trouble with VIBRANT even though the test runs have worked like they're supposed to.

I began with 150 bp .fastq reads, paired-end and demultiplexed for each of my samples. I used a target-capture/hybridization sequencing method specific to viruses for this assay. I have concatenated the .fastq files and then converted from .fastq to .fasta for use as input into VIBRANT. When I run the following command:

`VIROME_DIR="/projects/gibas_lab/UNCC-viral-panel"
sample_dir="${VIROME_DIR}/combined_samples/WW_CN_032323"
fastqs_dir="${sample_dir}/wastewater_samples/trimmed_ww_out/WW_paired/merged_WW"
outdir="${sample_dir}/VIBRANT_out"
mkdir -p ${outdir}
for i in `ls $fastqs_dir/*.fasta`
do
    echo "vibrant-ing $i"
    name=`basename $i | cut -f1 -d.`
python3 /projects/enviro_lab/software/VIBRANT/VIBRANT_run.py -i $i -folder "${outdir}" -virome
done`

I am getting, for each sample, a VIBRANT_xx directory, a vibrant run log, and intermediately, a parallel-run.temp, parallel-run.txt, and a four-out-count.txt file. When I look at the log files for each sample, the output says "No phages found. There were either no scaffolds at least 1000bp or 4 ORFs (set minimum size), or the input file (-i) format (-f) was not FASTA nucleotide. Exiting."

I am not sure where in my submission things are going awry and would love some assistance if possible!

Many thanks,

Lauren

AnantharamanLab / VIBRANT

VIBRANT not generating information in outfiles #92