Open bmansfeld opened 1 year ago
Hi Ben, thanks for this report! This might indeed be a bug. I see if I can reproduce the error. Any chance you can share your input data? Burkhard
Hey Burkhard, Thanks for looking in to this. The analysis was on our yet unpublished (preprint: https://www.biorxiv.org/content/10.1101/2023.03.22.533842v1) malus fusca genome. You can download the hap1 fasta from here: https://www.rosaceae.org/Analysis/15540543?pane=bio_data_2_rsc_assembly Let me know if there's anything else you need. Ben
Hi again, Love the
-a
option it really helps streamline any downstream pyhlogenetic analyses. I just wanted to note here something that at least in my hands seemed to be a bug.When running the following command
and then running FastTree (from bioconda v2.1.11 https://anaconda.org/bioconda/fasttree) I received the following error:
After further inspection several of the alignment rows had different lengths in most cases the number of
-
was different.I corrected this using an awk 1-liner extending the rows to 200 chars (to be on the safe side)
Running fasttree on this
genome_NLR.nbarcMotifAlignment.200.fasta
file yields no errors.Let me know if you think i am doing something wrong here or mis-interpreting something. But just wanted to report. Ben