Open Koen-vdl opened 1 month ago
How irritating -
(1) Does the analysis work if you specify a GTR model?
(2) Is there anything unusual about the *.tre.rooted
phylogeny (e.g. many near zero-length branches?)
One other thought - -T AUTO
might cause problems if there are concurrent processes on the same machine.
Thanks for getting back so quickly to me @nickjcroucher.
I added --model GTR
and obtained the same result.
As you suggested *.tre.rooted
indeed contains a lot of near zero branch lengths.
Did you remove --bestModel
when specifying GTR
? (sorry, I should have clarified that). It might be that there isn't sufficient information to fit the more complex model (although that seems unlikely), it might be worth starting with JC
to see if that can help identify the issue.
Hi @Nick, I tried what you suggested (with and without the tree-args) and got the same error
*** buffer overflow detected ***: terminated
Aborted (core dumped)
This is the full command I used.
run_gubbins.py $PREFIX-CLEAN_NoRef.aln --first-tree-builder iqtree \
--tree-builder iqtree \
--tree-args " -T AUTO" \
--first-tree-args " -T AUTO" \
--model-fitter raxml \
--iterations 10 \
--threads 62 \
--prefix $PREFIX \
--model GTR \
--first-model JC
I could upload the input alignment to my personal cloud space in case you wish to take a closer look:
Sorry, the alignment file appears to be corrupted (I have tried downloading it twice). Have you tried removing " -T AUTO"
(IQTREE2 will still be parallelised using the old -nt
flag - I am now updating this)? If that doesn't work, perhaps try using --mar
, in case it is the joint reconstruction that is causing the problem?
Hi Nick,
I'm using Gubbins v3.3.5 as indicated below:
After the first iteration during model fitting gubbins breaks with the following error:
I have not been able to work out why. I'm using
raxml
instead ofiqtree
during model fitting as I previously encountered the issue described here.Any help would be much appreciated.