Outgroups not added in align_selected_and_tree

[joyceem]

Hi Chris,

I'm having an issue with the align_selected_and_tree step. Up until then, everything runs fine, and I have all my cleaned sequences in the 09_sequences_from_qc_trees (inlcuding all internal outgroup sequences). However, when I go to run align_selected_and_tree step, all of my internal outgroup sequences are removed.

I can see from the log files that it identifies the internal outgroup sequences and the ones for which there are multiple copies (so it seems that the filter_internal_outgroups function works), but then it doesn't write any of them to my 10_sequences_from_qc_outgroups_added fasta files. I can't figure out why this would be.

I did have to reformat the sequence fasta headers from the output of CAPTUS to match the HybPiper format, so I could have made a mistake there? But otherwise I really don't know what's going on. I've attached the log file and some example fasta files from the 09 and 10 folder - any help would be really appreciated!

Many thanks, Lizzy cap_eg.zip

[chrisjackson-pellicle]

Hi Lizzy,

Ah, I think it's because you called the command with:

paragone align_selected_and_tree 09_sequences_from_qc_trees --pool 8 --threads 16 --trimal_gapthreshold 0.25 --generate_bootstraps

Instead of the folder 09_sequences_from_qc_trees, this command expects the folder 04_alignments_trimmed_hmmcleaned, as it will extract any needed internal outgroup sequences from the alignment files in this folder.

I've made the same mistake - I'll insert a warning if any outgroup sequences can't be found in the next update.

Cheers,

Chris

[joyceem]

Ah, I see!! My silly mistake. Thanks a lot for your help Chris :D

Cheers, Lizzy

On Thu, 30 May 2024 at 9:02 AM, Chris Jackson @.***> wrote:

Hi Lizzy,

Ah, I think it's because you called the command with:

paragone align_selected_and_tree 09_sequences_from_qc_trees --pool 8 --threads 16 --trimal_gapthreshold 0.25 --generate_bootstraps

Instead of the folder 09_sequences_from_qc_trees, this command expects https://github.com/chrisjackson-pellicle/ParaGone/wiki/Tutorial#step-4-phylogenetic-trees-from-selected-sequences the folder 04_alignments_trimmed_hmmcleaned, as it will extract any needed internal outgroup sequences from the alignment files in this folder.

I've made the same mistake - I'll insert a warning if any outgroup sequences can't be found in the next update.

Cheers,

Chris

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[chrisjackson-pellicle]

No worries!

[chrisjackson-pellicle]

Fixed in version 1.1.0