These are chat archives for dereneaton/ipyrad

Apr 2018
Apr 06 2018 07:10
@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.
Do you know how should I do to solve this problem? Thank you.
Nitish Narula
Apr 06 2018 13:58

Hi everyone. Can anyone help me troubleshoot this error:

2018-04-06 12:56:07,053     pid=109314     []    ERROR     EngineError(Engine '06ef7dae-c488c62846d2fdfb2fb81725' died while running task u'8e36d544-c4421e2c3faf9fb422c30082')
2018-04-06 12:56:17,375     pid=109314     []    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
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.
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!