These are chat archives for dereneaton/ipyrad

Nov 2018
Joel A. Mercado-Diaz
Nov 18 2018 20:12
Dear @isaacovercast @dereneaton: I am using ipyrad for the first time and decided to start practicing with the tutorials and confronted this error which other people have encountered in step 7: error in filter_stacks on chunk 416: IOError(Unable to open file (Unable to lock file, errno = 11, error message = 'resource temporarily unavailable')) . Following suggestions by @nspope , I reinstalled h5py via conda as a first step. The other idea of replicating the error outside ipyrad I couldn't do because no assemblyName>_across folder nor a .clust.hdf5was produced during my replication of the advanced tutorial. A .hdf5 file is actually produced (i.e. data1.hdf5), but its within within the iptutorial/data1_outfiles folder. About memory/disc space, how much space will I need for the assembly of the simulated rad_examples datasets in the tutorial? I am running this in 40 core shared server and using only 5 cores for the task. Thanks for any help!
Nov 18 2018 21:59
Joel, what happened after re installing h5py?
Did you solve the issue with step? I have the same problem as you.
Isaac Overcast
Nov 18 2018 23:08
@jamercadodiaz What kind of system are you on? Is it a cluster? What kind of disk are you running the assembly on? How much disk space is free? Is it a network filesystem? As much detail as you can give me about the hardware will be useful.
the simulated data is quite small so the amount of ram and disk for this assembly should be negligible.
My suspicion is the 'shared server' you're running on has an NFS filesystem which often has problems with hdf5 file locking: