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VIBRANT not generating information in outfiles #92

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lroppolo opened this issue Apr 3, 2024 · 1 comment
Open

VIBRANT not generating information in outfiles #92

lroppolo opened this issue Apr 3, 2024 · 1 comment

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@lroppolo
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lroppolo commented Apr 3, 2024

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

@KrisKieft
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Hi, VIBRANT is not meant to run on reads. It is intended for assembled scaffolds or genomes. Each of your input sequences are 150bp and the minimum threshold, which is extremely low already, is 1kb.

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