Using phylogenetic tools in v5.0

[jeffreybm]

Hi Jody,

I am interested in using the phylogenetic tools you had added to version 5. I quite dont understand how to use the functionality. If I run:
tb-profiler profile
--no_trim
--read1 ${reads_dir}/${sample}.trim.1.fastq.gz --read2 ${reads_dir}/${sample}.trim.2.fastq.gz
--prefix ${sample}
--call_whole_genome
--update_phylo
--dir tb_profiler_out

I get an error, see attached SRR7516395.errlog.txt
SRR7516395.errlog.txt

If I run without the --update_phylo flag run completes and there is an empty phylo.pb.lock file in results/

I assume we would need at least 3 samples to run on for a tree to be made, so I guess I dont understand how we would run the first sample and then update this phylo file with subsequent samples?

Thanks for the help!

Brendan