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sanger-pathogens / Roary

Rapid large-scale prokaryote pan genome analysis
http://sanger-pathogens.github.io/Roary
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Get a wrong core_gene_alignment.aln #584

Closed augustkx closed 1 year ago

augustkx commented 1 year ago

Hi! I get a wrong core_gene_alignment.aln output, where there is no sequence, only isolate names:

iso_485.100

iso_485.101

iso_485.102

iso_485.103

iso_485.104

I used the command in snakemake pipeline: roary -f roary -v prokka//gff -p 10 -e --mafft -g 700000 -z

I will appreciate it very much if you could give a hint where is wrong. Thanks in advance!

andrewjpage commented 1 year ago

What happens if you run the command outside of snakemake and put all the assemblies in the same directory? I can see your command is incorrect, mixing options at the end after the input files. Try just running: roary *.gff directly on the command line as a test.