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faircloth-lab / phyluce

software for UCE (and general) phylogenomics
http://phyluce.readthedocs.org/
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phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed not functioning #352

Closed sbabbbie closed 3 weeks ago

sbabbbie commented 3 weeks ago

I'm having an issue that I cannot resolve. It's the same issue someone had back in 2018, but the suggested fixes aren't working for me:

https://github.com/faircloth-lab/phyluce/issues/129

Basically, phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed doesn't work and I can't figure out why. The loading bar for trimming seems to be working fine, then suddenly I get the error:

"FileNotFoundError: [Errno 2] No such file or directory: '/Users/sbabbbie/Documents/UCE/backbone_tree_test/seed+mysequences_aligned_fragmentscollapsed_endstrimmed_stage2/uce-2175.fasta-gb'".

It doesn't seem to be making any fasta.gb files for any alignments as far as I can see, and I'm left with an empty output directory. Editing the phyluce.conf file as someone suggested on the linked thread didn't make a difference. I'm on an Apple M2 chip if that matters, but I installed following the instructions for the M series chips. Gblocks and Phyluce are both updated. Any advice?

brantfaircloth commented 3 weeks ago

Hi Spenser,

Gblocks does not work on any M-series chips, as far as I know. The source code is also not open, so we cannot recompile for an M-series. Your best best is trimal in place of Gblocks. Or run the Gblocks step on Linux (eg on the cluster).

-b

sbabbbie commented 3 weeks ago

That was so fast!! Thanks, Brant!