These are chat archives for dereneaton/ipyrad

24th
May 2018
Peter B. Pearman
@pbpearman
May 24 2018 11:58
Hello @isaacovercast , @dereneaton , I would like to echo the enthusiasm of @jrtrottablanc regarding the upcoming multi-threading of building the database for Step 6. We really appreciate the functionality of ipyrad, up to the limitations imposed by the single-thread implementation of step 6. There is a lot of population genomics that can be done on data sets with several hundred samples, and it will be great when ipyrad can handle them with sufficient speed to make it the go-to option. You have all the encouragement I can give you.
pedroamandrade
@pedroamandrade
May 24 2018 17:15

Hi everyone,

I'm sorry if this is a repeat question, but I couldn't find anything that solved my problem either here or in other websites. I'm starting to analyze a ddRAD-seq dataset with ipyrad, and I running into a problem in step 2, specifically cutadapt does not run. The log displays this error: ImportError: No module named cutadapt.scripts

I've searched for a solution but the only one I've found mentions the python version having to be up at least 2.6, but the server I'm using has 2.7.10. Otherwise I'm stumped... If anyone is willing to help out here are more details:

  • I'm running this on a user account on a remote server (without root access)
  • I installed conda locally, and edited .bashrc to append the miniconda2 directory (and this is working)
  • I installed both ipyrad and cutadapt with conda

Thanks!
Pedro