Closed cgmayers closed 4 years ago
Hi Chase
Thanks for the details, from the looks of things this should be resolved by the fix that was submitted for the previously reported issue. I've pushed out a new release yesterday with this fix in so would you be able to try updating to that and letting me know how it goes? I'd also be interested to know whether OG0000725 is successful or not this time. OrthoFinder should be fine in either case but it'd be interesting to know if there is an occasional & intermittent problem with the alignments.
All the best David
David,
This was extremely fortuitous timing! After updating to 2.4, the analysis completed successfully with no errors.
Thank you! Chase
That's great, thanks for letting me know!
Hi David,
I have encountered what seems to be the same problem as this thread and this more recent thread. OrthoFinder fails during MSA, producing (in addition to many normal orthogroup files) an empty orthogroup file and halting the program. First, I'll paste the log with error, then follow up with some more information below.
(I've bolded my text to make it stand out from log snippets, since I have some comments in the middle of two big chunks. This is my first time posting on GitHub so my formatting's clumsy.)
To explain some of the directories here, I've activated the conda environment "py37" which is running Python 3.7. Further system info is at the bottom of this post.
Like you predicted in the previous threads, an empty orthogroup file was produced in /Alignments_ids. I've attached the file from /Sequences_ids that has the same name (OG0000725.fa) as the empty 0KB file from /Alignments_ids (OG0000725.fa). It's had ".txt" added to it to allow uploading here.
OG0000725.fa.txt
Like you suggested in the previous thread, I ran
$ mafft --localpair --maxiterate 1000 --anysymbol OG0000725.fa > OG0000725.aln.fa
on this exact file, getting the following (apparently problem-free) result:In the most recent thread linked at the top, this was all fixed by simply running the analysis on another computer, but I don't have that luxury at the moment. I wonder if there's any clues in common between my data and the previous poster's? If it's a per-machine thing, it must be something about the local environment, not the data itself.
For full information, I have OrthoFinder 2.3.12 and I'm running Ubuntu 18.04.4 LTS in "Windows Subsystem for Linux" compatibility layer in Windows 10 64-bit (ver. 10.0.18362 Build 18362), with 32 GB RAM; cpu is i5-8350U; machine is Lenovo Thinkpad T480.
For good measure, I've zipped the entire folder (original input files and Orthofinder results) and attached it here, too.
RemoveIfHaveStop2_DelLastLine.zip
In the most recent thread linked at the top of this post, you mentioned looking for
Species_Tree/Orthogroups_for_concatenated_alignment.txt
, however this folder doesn't exist for me anywhere.Is there anything else useful I could provide?
Thank you for your time! Chase