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sanger-pathogens / Roary

Rapid large-scale prokaryote pan genome analysis
http://sanger-pathogens.github.io/Roary
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core_gene_alignment file only seems to have 2 of 21 samples #582

Closed Barrington-wustl closed 1 year ago

Barrington-wustl commented 1 year ago

roary -f Roary_Copy/Roary_Full -e -n -v -p 16 Roary_Copy/*.gff

this is the code I put in I got the core_gene_alignment file but it only has 2 samples in it 102_48_S1 and PAO1 but is missing the rest of the gff files image

I believe this is giving problems with making a phylogenic tree with RAxML giving the error

`(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`

andrewjpage commented 1 year ago

I'm guessing you've accidentally overwritten most of the files with a single file (based on the identical file sizes in your output).