These are chat archives for dereneaton/ipyrad

24th
Oct 2016
James Clugston
@Cycadales_twitter
Oct 24 2016 16:12
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@dereneaton @isaacovercast Hi guys, I am having a problem with the same run as I have mentioned before (sometime a few weeks ago) and I am getting some strange error during step six. After the strange issues last time I started the run from scratch but I am still getting error. Here is a screen shot from terminal. The run is ezRAD data for 150 PE read with about 80 samples so quite a large dataset. The run was created using version 0.4.2.
Isaac Overcast
@isaacovercast
Oct 24 2016 17:40
Hi @Cycadales_twitter. How much ram does the computer have that you're running this on? It looks like the computer is running out of ram and then indiscriminately terminating ipyrad processes.
Step 6 can be super memory intensive. It might help to try running with fewer cores (consume less memory overall), but then it would take longer to run. How many cores did you use with the run that crashed?
James Clugston
@Cycadales_twitter
Oct 24 2016 18:48
@isaacovercast I think each node has 8 cores and 32gb ram. I think its about 6 nodes in total on the cluster. We could give it more ram.
Isaac Overcast
@isaacovercast
Oct 24 2016 19:52
Yeah, if you can give it more ram that would help. I would try at least 64, but more if you can swing it.
James Clugston
@Cycadales_twitter
Oct 24 2016 20:30
@isaacovercast thanks Isaac I will give that a go. Quick question is the thing sorted now that if you interrupt a run you don't need to start back from where you started the command? otherwise this would mean I have lost yet another few weeks...
Isaac Overcast
@isaacovercast
Oct 24 2016 20:45
Hi James, Yes it's sorted out, you should be able to just run from step 6 since step 5 completed successfully.
James Clugston
@Cycadales_twitter
Oct 24 2016 21:06
@isaacovercast thanks Issac I appreciate your help man.