Open mlosilla opened 3 years ago
Dear @mlosilla,
The RELAX-scan
analysis is an add-on. It is not a part of the standard HyPhy
distribution. To use, assuming you have hyphy
installed
$git clone https://github.com/veg/hyphy-analyses
$cd hyphy-analyses/RELAX-scan
$/path/to/hyphy ./RELAX.bf --alignment ...
Best, Sergei
Hi Sergei,
I did as you suggested but the run failed after 1-2 seconds. I attach the error log.
Thanks errors.log
The error is similar to the first one reported here: https://github.com/veg/hyphy-analyses/issues/12
Dear @mlosilla,
I was able to reproduce the error. Will require a fix to RELAX-scan
. Stay tuned.
Best, Sergei
PS Fix issued. Do
$cd hyphy-analyses/RELAX-scan
$git pull
$/path/to/hyphy ./RELAX.bf --alignment ...
Thank you Sergei, that was super fast!
It seems to be running now, thank you very much!
I was wondering, does RELAX-scan support the option to include a synonymous rate variation (--srv Yes)?
Thanks Mau
Hi,
I can't figure out how to install and run RELAX-scan. I have downloaded and installed hyphy-analyses as explained in this ReadMe: https://github.com/veg/hyphy-analyses. All 21 tests executed by "make test" complete successfully.
But the only RELAX.bf file I get seems to be the standard RELAX test. When I run it as:
./HYPHYMP ./res/TemplateBatchFiles/SelectionAnalyses/RELAX.bf --alignment path_to_alignment/alignment.fasta
I get the error: Error:RELAX requires at least one designated set of branches in the tree. in call to assert(CUJAIACd.option_count>=2, error_msg); RELAX requires at least one designated set of branches in the tree. in call to assert(CUJAIACd.option_count>=2, error_msg);
Furthermore:
1) with the exception of FEL.bf, all the .bf files in hyphy-develop/res/TemplateBatchFiles/SelectionAnalyses/ have the same md5 hash as those in hyphy/share/hyphy/TemplateBatchFiles/SelectionAnalyses (this is where I installed hyphy (https://github.com/veg/hyphy), via conda install hyphy)
2) I can't find the .bf files for the tests listed in https://github.com/veg/hyphy-analyses : BUSTED-MH, BUSTED-SR, etc.
Clearly, I am doing something wrong. Could someone please provide me some guidance? I am installing on a computer cluster running CentOS7, and I don't have sudo privileges
Thanks