Running ViFi with Custom Reference Files

[DAWNkKim]

Hello,

I would like to use ViFi with a specific reference file that I have. Therefore, I'm referring to the following content:
`#Set up reference for alignment
HUMAN_REF="GRCh38"
HUMAN_REF_FILE_NAME="hg38full.fa"
for virus in "hpv" "hbv" "hcv"; do
if [ ! -d $REFERENCE_REPO/${virus} ]; then
echo "Reference for virus $virus is not downloaded. Contact the author to get access to the viral references."
else
HUMAN_VIRAL_REF="grch38_${virus}.fas"
echo "Building the ${HUMAN_REF}+${virus} reference"
cat $AA_DATA_REPO//${HUMAN_REF}/${HUMAN_REF_FILE_NAME} $REFERENCE_REPO/${virus}/${virus}.unaligned.fas > $REFERENCE_REPO/${virus}/${HUMAN_VIRAL_REF}
docker run -v $REFERENCE_REPO/${virus}/:/home/${virus}/ docker.io/namphuon/vifi bwa index /home/${virus}/${HUMAN_VIRAL_REF}

    #Build reduced list of HMMs for testing
    echo "Creating the list of hmms for testing in $VIFI_DIR"
    ls $VIFI_DIR/viral_data/${virus}/hmms/*.hmmbuild > $VIFI_DIR/viral_data/${virus}/hmms/hmms.txt
    ls $VIFI_DIR/viral_data/${virus}/hmms/*.[0-9].hmmbuild > $VIFI_DIR/viral_data/${virus}/hmms/partial_hmms.txt`

running command
docker run -v $REFERENCE_REPO/AB033550/:/home/AB033550/ docker.io/namphuon/vifi bwa index /home/AB033550/hybrid_hg19nAB033550.fas

However, the HMM and TRE files were not generated, so I tried running "ViFi/scripts/build_references.sh". I ran the following command on June 13, but it still hasn't completed.

running command
sh /home/kde/PROJECTS/VirusIntegrationTools/download/ViFi/scripts/build_references.sh /home/kde/PROJECTS/VirusIntegrationTools/download/ViFi/viral_data/AB033550/hybrid_hg19nAB033550.fas /home/kde/PROJECTS/VirusIntegrationTools/download/ViFi/viral_data/AB033550/output hybrid /home/kde/PROJECTS/VirusIntegrationTools/download/ViFi/scripts

If it's appropriate to use "build_references.sh" to run ViFi with my reference files, why is it taking so long? Is there a solution?

Thanks