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Species not found in gene family #54
Description
Hi folks,
I'm trying to run CAFE5 on a dataset that I formatted based on the output of Orthofinder (attached - hymenoptera_orthogroups.txt), and the binary, rooted, ultrametric tree (attached - hymtree_ultrametric.txt). I keep ending up with a weird error upon running this command:
cafe5 -i hymenoptera_orthogroups.txt -t hymtree_ultrametric.txt
Command line: cafe5 -i hymenoptera_orthogroups.txt -t hymtree_ultrametric.txt
Tric was not found in gene family x
Any thoughts or advice would be greatly appreciated!
Thanks!
Arun
hymenoptera_orthogroups.txt
hymtree_ultrametric.txt
Activity
benfulton commentedon Mar 24, 2021
This generally indicates that your file has Windows-style line endings. You can use the Linux program dos2unix to fix the line endings.
arunsethuraman commentedon Mar 24, 2021
Goodness - such a rookie error on my part! Thank you! This fixed the issue instantly.
nahumemss commentedon Oct 18, 2021
Hi
I have the same issue, but the dos2unix doesn't work and the same message appear to me.
=(
benfulton commentedon Oct 26, 2021
Can you share your tree and family files?
nahumemss commentedon Oct 30, 2021
I changed the gene files for .csv and works
kat-king commentedon Jul 27, 2022
Hi, I'm having this same issue but the two solutions above don't work for me. Any suggestions?
benfulton commentedon Jul 27, 2022
Can you share your tree and family files?