Stephane Guindon
Stephane Guindon
Indeed... The github version works fine with the --sequential and -q options but the bioconda one seems to fail miserably... Maybe @epruesse has an idea?
--sequential aka -q set the value of io->interleaved to NO (the default being YES). PhyML then calls Read_Seq_Interleaved(io) (in case io->interleaved == YES) or Read_Seq_Sequential(io) (when io->interleaved == NO). Those...
I was able to reproduce the bug on ubuntu 18.04. I haven't tried any other architecture.
Please use the following command instead: mpirun -np 2 ./phyml-mpi -i trim2_outgroup_dropDupli.phy -d aa -q -b 100 -m LG -a 0.749 -f m --pinv 0.05
Are you 100% sure the machine you're using here has enough RAM et CPUs to run 20 analyses in parallel? I would try try -np 10 just to see...
Dear Felix, The two constraint trees you give seem fine to me. PhyML should be able to use either of them. It could be the case, however, that the input...
Sorry for the (very) late response... I'm aware of this issue. Is there any specific reason why you would use this compilation option?
I see... Versioning with SIMD extensions is giving me nightmares. The "problem" with the --disable-native option is that one cannot completely discard SSE as some core functions of glibc rely...
I'm sorry I do not have much time these days to look into this. I'll try my best next week but in the meantime I suggest you use an older...
I was unable to reproduce this issue with the latest stable release (Summer 2020) and the following command-line options: ./phyml -i aln.phy -d aa -m custom --aa_rate_file=./model.PAML Did you use...