First-split-outgroup function does not work

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Pertseva Margarita

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Dec 15, 2020, 10:00:10 AM12/15/20

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Dear ETE3 group,

I’m trying to build a phylogenetic tree using a standard_phyml command. I have to root/outgroup the tree on a sequence present in a fasta file which is called ‘germline’.
Example fasta:

>CL4197840

CAGGTCCAACTGCAGCAGTCTGGGGCTGAGCTTGTGAAGCCTGGGACTTCAGTGAAGATGTCCTGCAAGTCTTCTGGCTACACCTT

>germline

CAGGTCCAACTGCAGCAGCCTGGGGCTGAGCTTGTGAAGCCTGGGGCTTCAGTGAAGATGTCCTGCAAGGCTTCTGGCTACACCTT

I’m using the command below:
ete3 build -w standard_phyml -n cluster1.fasta --first-split-outgroup germline -o cluster1_PHYML

But always getting an error: “TaskError: Unknown seqs cannot be used to set first split rooting:”

I also tried to insert the germline nucleotide sequence directly into the command line after --first-split-outgroup, but it gave me the same error and I could not find any solution online.

Would be really grateful for your help!! Thanks!

Best regards,
Margarita

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