These are chat archives for dereneaton/ipyrad

4th
Jan 2019
tommydevitt
@tommydevitt
Jan 04 19:59
@isaacovercast I just installed ipyrad and conda on a new HPC system and am trying to run through the example Pedicularis dataset to make sure everything is working. However, when I tried to download the data using
conda install -c bioconda sra-tools entrez-direct
ipyrad --download SRP021469 example_empirical_data/
I was getting an error about toytree not being installed:
Error: tetrad requires the dependency 'toytree', which we haven't yet
included in the ipyrad installation. For now, you can install toytree
using conda with the following command:
conda install toytree -c eaton-lab
Tried that, it didn't work so I downgraded toytree
conda install toytree toytree=0.1.16 -c eaton-lab
Now when I try to download I'm getting
Fetching project data...
Empty DataFrame
Columns: [Db value not found in fetch input]
Index: []
Exception in run() - index 29 is out of bounds for axis 0 with size 1
Download failed. Exiting.
Any ideas? Thanks.
tommydevitt
@tommydevitt
Jan 04 20:38

@isaacovercast Edit: tried running step 7 on my own dataset and got this error:

Step 7: Filter and write output files for 143 Samples
[####################] 100% filtering loci | 0:02:10

Encountered an error (see details in ./ipyrad_log.txt)
Error summary is below -------------------------------
error in filter_stacks on chunk 31262: EngineError(Engine '8d8e9402-be14b98e5c056b09163f5cff' died while running task u'd304b6ae-b35c2d0a706cfa3dd10d9cb2')
warning: error during shutdown:
[Errno 3] No such process

Not sure why the engines are dying.