Index genome not working in Tracy

I’m trying to follow the variant calling guide for Tracy.

I have a viral genome just as a fasta file, and when I try to call variants like this:

tracy decompose -v -a cmv -r CMVrefGenome.fasta -o oututfile inputfile.ab1

It tells me the genome needs to be shorter than 50kb, or indexed. I tried running this with a smaller fasta file only including the part I’m interested in, and this code worked. But when I tried to put the vcf files (converted from the bcf files) into IGV, they can’t be read (I get the error (“filename.vcf null”). I don’t understand why they can’t be read. Therefore, I am trying this again but instead of cutting out a part of the genome, I want to use the exact same reference genome file in IGV, and maybe this will work. Therefore, I need to index the genome instead of cutting out just a piece. Tracy talks about genome indexing here:

But when I try this with my fasta file, it says “Done” but then no file appears in the folder. On this page they say an fm9 file should appear with this command (

tracy index -o CMVrefGenome.fasta.fm9 CMVrefGenome.fasta

I have also tried using samtools:

samtools faidx CMVrefGenome.fasta

This produces a file called in the same directory, however when I try to run the tracy variant calling as above, I still get the error saying the genome is too long or needs to be indexed. I’m completely out of ideas now on how to solve this

Thanks in advance

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