Closed yuemeanshappy closed 1 year ago
Hi Yue,
Thank you for writing and providing the necessary information, such as the software version and data files.
I ran OrthoSNAP 10 times on the data and got the same output each time. I'm sorry, but I am unable to recapitulate your issue. Perhaps there is some issue with version controls. If you haven't, I recommend installing OrthoSNAP into a virtual environment.
Please let me know if the issue persists, otherwise I will wait a few days before closing the issue.
All the best,
Jacob
Hi Jacob,
Thank you so much for your quick response! I figure it out. The issue does not persist.
Thanks again, Yue
Great - happy to hear it!
Hi Jacob,
I used orthosnap (0.1.1) to identify SNAP-OGs from a group of orthogroups, but found that the results sometimes are not reproducible in some orthogroups, like the one (OG0010358.fa) I provided here.
The command line I used was
orthosnap -f OG0010358.fa -t OG0010358.fa.contree -op ./results
and it identified one SNAP-OG each time. But the SNAP-OG identified in the first round (first-round-OG0010358.fa.orthosnap.0.fa
)was different from the one identified in the second round (second-round-OG0010358.fa.orthosnap.0.fa
). All files attached at the end. (The.fa
and.contree
are not supported by GitHub, so I stored them in.txt
to upload.)Before running orthosnap, I used OrthoFinder to identify orthogroups, used MAFFT and ClipKit to trim the alignment, and used IQ-Tree to build the gene tree.
Any thoughts are much appreciated!
Best, Yue
first-round-OG0010358.fa.orthosnap.0.fa.txt OG0010358.fa.contree.txt OG0010358.fa.txt second-round-OG0010358.fa.orthosnap.0.fa.txt