These are chat archives for dereneaton/ipyrad

20th
Sep 2017
arminf
@arminf82
Sep 20 2017 14:35

@isaacovercast "SplitsTree is capable of reading phylip files" -> I tried to load the phylip files into splitsTree but it did not work: "Import failed: unknown format or error in file (e.g. illegal characters or multiple occurrences of same taxon name.) Nexusfile from same dataset is working.

Strange...

arminf
@arminf82
Sep 20 2017 14:44
I love ipyrad but I canĀ“t really help with much programming but I wanted to ask again ;-), if somebody is working on an implementation of GBS2ploidy? (https://groups.google.com/forum/#!topic/pyrad-users/3kgW6ypKEOI)
Isaac Overcast
@isaacovercast
Sep 20 2017 15:49
@bioballs No progress on the ploidy estimation, bigger fish to fry at the moment.... If you can get me more information about why splitstree is rejecting the phylip file i can look into it. I don't know anything about SplitsTree.
tommydevitt
@tommydevitt
Sep 20 2017 19:22

@isaacovercast @dereneaton OK, I removed the profile argument, submitted the batch job to start the ipcluster, and am now trying to connect to that cluster and print how many cores are available, as described in http://ipyrad.readthedocs.io/HPC_Tunnel.html. I did

import ipyrad as ip
import ipyparallel as ipp

## connect to the client
ipyclient = ipp.Client

## print how many engines are connected
print(len(ipyclient), 'cores')

and got

TypeErrorTraceback (most recent call last)
<ipython-input-14-75d53df3a4f7> in <module>()
      6 
      7 ## print how many engines are connected
----> 8 print(len(ipyclient), 'cores')
      9 
     10 ## or, use ipyrad to print cluster info

TypeError: object of type 'MetaHasTraits' has no len()
Isaac Overcast
@isaacovercast
Sep 20 2017 19:48
## connect to the client
ipyclient = ipp.Client()
try that.
tommydevitt
@tommydevitt
Sep 20 2017 19:59
That worked (in that there's no longer an error) but I'm not connected to the ipcluster instance I submitted in a separate batch script. I'm only seeing the 24 cores I have in my script to start the jupyter notebook.
vieves
@vieves
Sep 20 2017 22:27
Is there a way to run an assembly and only genotype SNPs that have been identified from a previous assembly? I have an assembly made from a subset of my samples. Now I want to make an assembly that includes all of my samples, but only with the variable sites that were called based on the subset.