These are chat archives for dereneaton/ipyrad

Oct 2017
Oct 05 2017 00:07
@isaacovercast I used -b to create a new branch and re-ran ipyrad from step 4 with max_alleles_consens = 1
Ollie White
Oct 05 2017 13:32

Hi @isaacovercast, I think my disk space should be sufficient. I am running ipyrad on a compute node of our University HPC. Below is the tail of by .o file after running one of the scripts from step 3 through to 6.

Requested resource limits are neednodes=1:ppn=16,nodes=1:ppn=16,pmem=4000mb,walltime=48:00:00
Used resource limits are cput=00:13:07,mem=285480kb,vmem=1311520kb,walltime=03:05:44

Not sure what is happening but it seems to work fine when I run each branch one at a time

Isaac Overcast
Oct 05 2017 16:20
@rfolkert Yes, that's true. I've never tried setting these values to 0, but there's no reason that wouldn't work.
@Ollie_W_White_twitter Disk space may look fine, but sometimes clusters have quotas imposed per user. Not sure if that's the issue. So you got everything to run fine now?
Isaac Overcast
Oct 05 2017 16:37
@congliu0514 I have no idea why this would happen. can you email me the params files for both the runs and one of the .consens.gz files from the _consens directory for each of the runs.
Oct 05 2017 21:41
@eachambers that's an error from the HDF5 library (h5py is the python package wrapping this library). As a first step try reinstalling h5py through conda. You might also try opening a connection to a file with h5py to see if you can replicate the error outside of ipyrad ... for example, go to the <assemblyName>_across output folder, in which there should be a file called assemblyName.clust.hdf5. Then in Python REPL:
import h5py
h5py.File("assemblyName.clust.hdf5", 'r')