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
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?
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