interaction QTL mapping gives MKL error

[broadinstitute]

interaction QTL mapping gives MKL error

[francois-a]

Hi Jack,

Yes, it seems like some of the required library files are not available/not in the path. Can you share the full stack trace to see where this is needed? I typically use OpenBLAS on Ubuntu and haven't run across any issues like this -- can you try building/installing numpy with OpenBLAS?

[jackhump]

sorry for delay,
this is all I get in the standard error:

  File "/sc/arion/projects/als-omics/QTL/NYGC_Freeze02_European_Feb2020/QTL-mapping-pipeline/Snakefile", line 420, in __rule_tensorQTL_cis
  File "/sc/arion/projects/als-omics/conda/envs/QTL-pipeline/lib/python3.7/concurrent/futures/thread.py", line 57, in run

[francois-a]

Can you run the command outside of the pipeline wrappers you're using? Or in a jupyter notebook?

[jackhump]

Hi Francois,

I've done a bit more sleuthing on this. I had installed numpy with OpenBLAS in tensorqtl conda environment using the following commands, from here: https://docs.anaconda.com/mkl-optimizations/

conda install nomkl numpy scipy scikit-learn

The MKL error was occurring because of a conflict with python in another conda environment that I was activating before I activated the tensorqtl environment, so just running "module purge" before I ran the tensorqtl command stopped this error. I hope this will be a useful lesson for other users.

Of note, I now realise this error was occuring only when I ran interaction QTLs in cis mode, but not in cis_nominal. If I'm not mistaken, there is no need to run interaction QTLs using the cis pass, because the resulting cis_qtl.txt.gz does not include the beta and P for the g*i term, correct?

[francois-a]

I'm glad that resolved it.

Yes, interactions can only be used with map_nominal. There is no permutation scheme for map_cis that would provide an adequate null.

I'll add a check to make sure interactions aren't parsed for map_cis -- what's the command you tried to run?