These are chat archives for dereneaton/ipyrad

15th
Nov 2017
asassone
@asassone
Nov 15 2017 16:20 UTC
@dereneaton @isaacovercast I am trying to run bucky and I am having problems, when trying to run b.write_nexus_files(force=True)
This error appered and 0 nexus file are wrote. I tryed with different datasets and upgrading ipyrad version but I can not fix the problem.
Warning: encountered an error in the alleles file format. This is a bug that was fixed in v.0.7.2. Rerun step 7 on this data set to ensure that the alleles file is properly formatted.
Can you help me?
Deren Eaton
@dereneaton
Nov 15 2017 16:43 UTC
hi @asassone , this error message is usually raised if the .alleles file is improperly formatted, which could occur if you made the file using an earlier version of ipyrad (<0.7.2) since we had a bug in the code for a little while. Is that the case for your input .alleles file? If so, you will need to rerun step 7 using an updated version of ipyrad to re-generate the alleles file.
asassone
@asassone
Nov 15 2017 16:45 UTC
@dereneaton It is not the case, and I have already re-run step 7 with the latest version.
Deren Eaton
@dereneaton
Nov 15 2017 16:47 UTC
hmm, ok, I'll check it out.
Jenny Archibald
@jenarch
Nov 15 2017 19:17 UTC

@dereneaton @isaacovercast First, thanks so much for your help getting bpp running! I used Isaac's instructions about a week ago:

git clone https://github.com/dereneaton/ipyrad.git
conda-build ipyrad/conda.recipe/bpp/
conda install --use-local bpp

The analysis is still running, whereas before it ended almost instantly. There are also MCMC files now in the analysis folder, unlike before. So, it's taking some time, but seems to be working?

However, I now seem to have a similar problem getting STRUCTURE to work. It gave a nearly identical error:

("structure: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by structure)\n", None)

So, second: how do I fix it this time? I'm guessing it's something similar, but I am pretty ignorant on what these commands are actually doing, and so I was wary of just adjusting them without checking first. For example, it looks like last time git clone made a separate copy of ipyrad near my original copy, and I'm not sure why that was needed, or whether I need to do it again. I'd appreciate it if you have time to give more instructions.

Deren Eaton
@dereneaton
Nov 15 2017 19:33 UTC
Hi @jenarch, weird, I'm still trying to figure out this glibc stuff. If it worked for bpp it should work for structure, I suppose. I shouldn't hurt to try. You will not need to re-clone the ipyrad repo, just replace bpp with structure and run the same command.
Then you should be able to just type structure in a terminal to call the binary.
Jenny Archibald
@jenarch
Nov 15 2017 20:08 UTC
@dereneaton Thanks for the quick reply! I gave conda-build ipyrad/conda.recipe/structure/ a try and it responded with an error including
Error: HTTP 404 NOT FOUND for url <http://pritchardlab.stanford.edu/structure_software/release_versions/v2.3.4/structure_kernel_source.tar.gz>
Looking online, that website does not seem to exist now, and instead perhaps this one is appropriate?
http://web.stanford.edu/group/pritchardlab/structure_software/release_versions/v2.3.4/release/structure_linux_console.tar.gz
Could you tell me how to deal with that?
Isaac Overcast
@isaacovercast
Nov 15 2017 20:18 UTC
@jenarch I fixed the conda recipe for structure. Clone the repo and try again
Jenny Archibald
@jenarch
Nov 15 2017 21:36 UTC
@isaacovercast @dereneaton Thanks! That seems to have fixed it. Structure is running now.