These are chat archives for dereneaton/ipyrad

3rd
Feb 2017
Emily Warschefsky
@ewarschefsky_twitter
Feb 03 2017 00:07

Hey @dereneaton and @isaacovercast : I am trying to merge workflows after step 1 and I keep getting :

-------------------------------------------------------------
  ipyrad [v.0.5.9]
  Interactive assembly and analysis of RAD-seq data
 -------------------------------------------------------------

  Merging assemblies: ['params-LibD.txt', 'params-LibC.txt']
  loading Assembly: LibD
  from saved path: /scratch/ewars001/ipyrad/Lane2/LibD/LibD.json

    Error: Steps >1 () requested but no current assembly found - /scratch/ewars001/ipyrad/Lane2/LibD/LibD

Help?! The filepath is correct, so I don't understand why it can't find it. I have tried relative vs absolute filepaths and that does not seem to change the result...

Isaac Overcast
@isaacovercast
Feb 03 2017 15:44
Hi @ewarschefsky_twitter Can you copy and paste the ipyrad command you're running? I have a suspicion of what the problem is, there was somebody with something similar recently.... One thing to doublecheck is that your project_dirs are set to absolute paths (this is the second entry in the params file).
Isaac Overcast
@isaacovercast
Feb 03 2017 15:59

@ajbarley2_twitter Are you sure you're importing the baba module correctly?

>>> import ipyrad.analysis.baba as baba
>>> stats, boots = baba.baba(handle, test, mindict, 1000)

works for me. Are you updated to the latest version? 0.5.15?

Emily Warschefsky
@ewarschefsky_twitter
Feb 03 2017 16:50

Hey @isaacovercast - I think fixing the paths of the project_dirs has solved that issue. One other issue that I am seeing is that a lot of times the step 1 runs fail with this error:

Encountered an unexpected error (see ./ipyrad_log.txt)
  Error message is below -------------------------------
[Errno 2] No such file or directory: './tmp-step1-count.fq'

If I rerun them, they work fine..

Isaac Overcast
@isaacovercast
Feb 03 2017 20:20
That's odd behavior. This is a temporary file that gets created during the process of estimating the size of the raw data. This error would only ever happen if the tmp file didn't get created for some reason (either no space left on disk or no write permissions for the directory you run ipyrad out of). This doesn't explain why sometimes it will work and sometimes it won't.... Not sure. Are you on a cluster?
Emily Warschefsky
@ewarschefsky_twitter
Feb 03 2017 20:23
yes - I am on a cluster. I'm submitting multiple jobs through a loop, and some will run while others don't. Where does the temporary file get created?
if it's in the working directory rather than the project_dir that could be an issue
Deren Eaton
@dereneaton
Feb 03 2017 21:24
@ajbarley2_twitter btw, many notebooks in the test directory are still in development, and could change. They'll be linked to in the "analysis tools" section of the documentation when they are more stable. That's cool that you're trying it out though.
Isaac Overcast
@isaacovercast
Feb 03 2017 21:44
@ewarschefsky_twitter The temp file gets created in the directory that ipyrad is run from. I will fix it so it gets created in project_dir.
@ewarschefsky_twitter Fixed. This change will go out with the next release. You could clone the git repo if you want it now...