Concatenate alignments does not work with phylip-extended format alignments

[brantfaircloth]

          the phyluce_align_format_nexus_files_for_raxml not works for phylip in this code 

phyluce_align_concatenate_alignments \ --alignments mafft-gblocks-70p \ --output mafft-gblocks-70p-raxml \ --log-path log --phylip

Originally posted by @rbolem in https://github.com/faircloth-lab/phyluce/issues/220#issuecomment-1639052157

[rbolem]

The phyluce _align _format nexus for raxml is automatically creating the output into a phylip format without using the log path log — phylip.

I’m I correct??

thanks

[brantfaircloth]

This should be corrected in the new version of code that I just uploaded. You will need to run like so:

phyluce_align_concatenate_alignments --alignments some-alignments --input-format phylip-relaxed --output concatenated_result --nexus

phyluce_align_concatenate_alignments --alignments some-alignments --input-format phylip-relaxed --output concatenated_result --phylip

The logging seems to be working as expected but you must make a directory to hold the log files first, and then use that directory as the --log-path.

[rbolem]

phyluce_align_concatenate_alignments is not working

[brantfaircloth]

Have you updated to the new version (1.7.3) versus 1.7.2? And if you have and it is still not working, I’m going to need some details about how it is not working. I tested and it seems to function correctly.

[rbolem]

updated the version. Thanks

[rbolem]

Had raxml-ng instead of raxmlHPC-PTHREADS-SSE3.

Please help me with these steps such as 1. raxmlHPC-PTHREADS-SSE3 -m GTRGAMMA -N 20 -p 772374015 -n BEST -s mafft-gblocks-70p.phylip -o menmol1 -T 10 raxml/raxmlHPC-PTHREADS-SSE3 -m GTRGAMMA -N autoMRE -p 772374015 -b 444353738 -n bootrep -s mafft-gblocks-70p.phylip -o menmol1 -T 10

my code: raxml-ng --msa mafft-gblocks-70p-raxml.phylip --model GTR+G --bootstrap 20 --bs-t 772374015 --threads 16 --tree pars{10} --prefix BEST

for the code above how much itll take to complete the run? I'm attaching the output file. please look into that let me know is it correct or not.I'm confused that run was ended or not. BEST.raxml.log

2. as I'm using raxml-ng, help me with the following code
   raxmlHPC-SSE3 -f b \ -m GTRGAMMA \ -t RAxML_bestTree.BEST \ -z RAxML_bootstrap.bootrep \ -n FINAL -o menmol1.

Looking forward.

Thanks.