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amkozlov / raxml-ng

RAxML Next Generation: faster, easier-to-use and more flexible
GNU Affero General Public License v3.0
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TOO FEW SPECIES #148

Closed Barrington-wustl closed 1 year ago

Barrington-wustl commented 1 year ago

Roary ran successfully as far as I can tell but now when I am running RAxML to make the phylogenic tree

this is what I ran

`(base) marshall@DESKTOP-LMRPD85:~$ raxmlHPC -s /home/marshall/Roary_Copy/Roary_Full/core_gene_alignment.aln -n Trikafta_Tree.txt -m GTRCAT -f a -x 123 -p 256 -N autoMRE -T 16 Use raxml with AVX support with overriden number of threads

RAxML can't, parse the alignment file as phylip file it will now try to parse it as FASTA file

TOO FEW SPECIES`

is there something obvious that I am missing?

Barrington-wustl commented 1 year ago

I have 21 samples and I have seen this program run with less

amkozlov commented 1 year ago

Hello, please check that your input file is a valid PHYLIP or FASTA ailgnment. It looks like a formatting issue.

amkozlov commented 1 year ago

If the issue still exists, please post to the RAxML google group (note you are using standard-RAxML and not raxml-ng here).