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churchill-lab / scBASE

A set of tools for accurate quantitation of single-cell allele-specific expression
https://churchill-lab.github.io/scBASE/
MIT License
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StanModel went wrong. #2

Closed heyuan7676 closed 5 years ago

heyuan7676 commented 5 years ago

Description

I'm trying to run scBASE with test input file. I went through all the step until scbase run-mcmc, and it said "Something went wrong while unpickling the StanModel". I got an empty output npz file.

What I Did

  scbase collate --counts -t input_test/geneID.txt --name input_test.txt input_test input_test/input_test.loom
  scbase select --min-read-count 1 --min-cell-count 1 input_test/input_test.loom 
  scbase run-mcmc input_test/input_test.loom -o input_test/output

The error msg is like:

Quantifying allele-specific expression in each cell
ASE model file: /Users/Yuan/Documents/BLab/scASE/scBASE-master/scbase/stan/zoibb.pkl
No module named 'stanfit4anon_model_0ce37513fbd552303fd9f1659d6b568d_8906517153169263311'
Something went wrong while unpickling the StanModel. Consider recompiling.
TGX model file: /Users/Yuan/Documents/BLab/scASE/scBASE-master/scbase/stan/pg.pkl
No module named 'stanfit4anon_model_14f98a31e12bc2325a7568074a7c0ece_6870842214747300932'
Something went wrong while unpickling the StanModel. Consider recompiling.
Genes from 0 to 3 (0-based indexing)

I tried re-installing pystan, it showed:

conda install pystan
Collecting package metadata (current_repodata.json): done
Solving environment: done

# All requested packages already installed.

Please help! Thank you!

Best, Yuan

heyuan7676 commented 5 years ago

Rerunning python setup.py install solved the problem. Thank you!

Best, Yuan