These are chat archives for dereneaton/ipyrad

28th
Jan 2019
LinaValencia85
@LinaValencia85
Jan 28 15:38
@isaacovercast not yet... It stops on s6 in the indexing step. And I am not able to get s7 to work. I get this error "ImportError: libhdf5.so.10: cannot open shared object file: No such file or directory"
tommydevitt
@tommydevitt
Jan 28 16:13

@isaacovercast Spoke too soon. When running step 3, I get the following error:

  Step 3: Clustering/Mapping reads
  [####################] 100%  dereplicating         | 0:00:02  
  [####################] 100%  clustering            | 0:00:02  
  [####################] 100%  building clusters     | 0:00:02  
  [####################] 100%  chunking              | 0:00:40  

  Encountered an unexpected error (see ./ipyrad_log.txt)
  Error message is below -------------------------------
EngineError(Engine 'd8b33efd-15029c64da1c4f4414dcb82a' died while running task u'ce2344ed-088d324491c7a99582ae0616')
warning: error during shutdown:
[Errno 3] No such process

You mentioned you thought this might be a memory issue. I've tried it with up to 192GB RAM. The data are from the ipsimdata tutorial. What do you think?

joqb
@joqb
Jan 28 17:59
Hi all,
I have a question not directly related to ipyrad but I want to obtain a file formatted like the u.snps.phy files from ipyrad. I have a bunch of loci each aligned across multiple individuals and species and I would like to sample from each locus a single SNP.
Does anyone know a way to do this?
Thanks in advance
Isaac Overcast
@isaacovercast
Jan 28 18:49
@TimBoeh Hi Tim. The libcrypto thing is a new problem caused by a version change of a dependency. There's a fix here: dereneaton/ipyrad#319
@LinaValencia85 This is normally a dependency issue. I'd bet removing your conda install and starting from scratch with a new conda install will fix this.
@tim-oconnor @Jamie_Bio_twitter Yeah, sorry I'm behind on things a bit. This is still on my stack, will try to get to it this week.
Todd Pierson
@twpierson
Jan 28 21:35
@isaacovercast : Don't mean to pile on, but I'm having the same problems as @tim-oconnor and @Jamie_Bio_twitter. Thanks in advance for your work to fix these things!