Closed rsiani closed 10 months ago
Dear @rsiani,
Could you please share the input files (raxml.bestTree
and H.list
)? I'll be happy to take a look, otherwise I won't be much help.
Best, Sergei
Dear @spond, I uploaded the file to gist here: files. Let me know if you can get them, first time sharing via gist.
Bests, Rob
Dear @rsiani,
You label file has an extra space at the end of each line so instead of "GCA_000143225_03002"
the labeler was looking for "GCA_000143225_03002 "
.
I'll add some code to the script to strip out trailing spaces, but simply deleting those from your H.list
file should do the trick for now.
Best, Sergei
Oh, thank you very much. I should have thought of looking for horses but went straight for the zebra...
Dear @rsiani,
I am glad you showed me this example! Making a minor scipt adjustment for the next update to deal with trailing spaces will probably save users a few hours of frustration.
Best, Sergei
Hi, I have been experiencing a weird problem with the labelling.
hyphy ~/hyphy-analyses/LabelTrees/label-tree.bf --tree raxml.bestTree --label H --list ../H.list --output H.tree
I checked several times and the label are correct. However I noticed the also running
grep -F -f host.list flhc.raxml.bestTree
does not return any match. So if that is called in the background I am a bit confused as to what is going on. Running grep on single lines correctly return the matches. Any idea what could be the issue? The only thing I am not sure is whether there might be duplicate sequences, but usually alignment tools remove those from the input (so before I construct the three).
Thanks