I am having trouble with BCF tools not calling a consensus sequence, despite passing the bowtie threshold, and having adequate depth. Is this a problem others are running into? It is not happening all of the time. Attached is an out file.

In your out file it doesn't seem to be any error. What do you mean by "not calling a consensus sequence"? There's not any consensus.fasta file? Is the consensus exactly the same as the reference? The consensus has all Ns instead of nucleotides?

Here is my Nextflow log. There is not a consensus fasta file, or A BCF tools file. That is why I didn't think BCF tools was occuring. I don't have any way to know if the consensus is the same as the reference, but it is definitely possible. Which Config file do you want?

Can you send me the files in your

pipeline_info

folder and your

multiqc_report.hmtl

file? Seems like some of the processes are not being executed. Do you have the .vcf.gz variants files? Or you don't have them either?