These are chat archives for dereneaton/ipyrad

6th
Apr 2018
YAO Xin
@danielyao12
Apr 06 2018 07:10
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@eaton-lab Hi Eaton, I got error message when I was going to download example data in the tutorial 'Eaton & Ree (2013) single-end RAD data set' . Here is the screenshot.
Then, I guess that would because I didn't use the full path in workdir. After I add the full path, I got different error.
image.png
Do you know how should I do to solve this problem? Thank you.
Nitish Narula
@nitishnarula
Apr 06 2018 13:58

Hi everyone. Can anyone help me troubleshoot this error:

2018-04-06 12:56:07,053     pid=109314     [assembly.py]    ERROR     EngineError(Engine '06ef7dae-c488c62846d2fdfb2fb81725' died while running task u'8e36d544-c4421e2c3faf9fb422c30082')
2018-04-06 12:56:17,375     pid=109314     [assembly.py]    ERROR     shutdown warning: [Errno 3] No such process

It happened after the "chunking" substep of step 3 finished. Is this related to memory? Thank you.

Isaac Overcast
@isaacovercast
Apr 06 2018 16:18
@danielyao12 sra fetching works fine for me, i just tested it. The error says it can't find the directory you're specifying, so maybe you don't have write access? Check your permissions on that directory.
@nitishnarula Hi Nitish, yes this is almost certainly a memory error. Engines dying is a common symptom of needing more RAM. We recommend around 4GB per core, so you can either allocate more RAM or reduce the number of cores you're running on.
argastaldi
@argastaldi
Apr 06 2018 16:46
Hi, I am new to ipyrad. I did the introductory tutorial yesterday and all went well. I am now trying to run ipyrad CLI with a subset of my ddRAD dataset, and I am getting stuck on step 6. During the "aligning indels" step it encounters the following error: "TypeError(Can't broadcast (8, 1982, 156) -> (8, 511, 156))". Do you have any ideas what might be causing that? Thanks!