diff options
| author | zsloan | 2022-09-28 12:59:43 -0500 |
|---|---|---|
| committer | GitHub | 2022-09-28 12:59:43 -0500 |
| commit | c9b102a459bc11be39ac20fa15539c3e2628d918 (patch) | |
| tree | 4a9172e51fc606b8788c42a9ad071114a84ec4cd | |
| parent | 7a48d26d11362472631becf189606c55019481ef (diff) | |
| download | gn-gemtext-c9b102a459bc11be39ac20fa15539c3e2628d918.tar.gz | |
Create phenotype-correlation-error.gmi
| -rw-r--r-- | issues/phenotype-correlation-error.gmi | 19 |
1 files changed, 19 insertions, 0 deletions
diff --git a/issues/phenotype-correlation-error.gmi b/issues/phenotype-correlation-error.gmi new file mode 100644 index 0000000..1d5fe23 --- /dev/null +++ b/issues/phenotype-correlation-error.gmi @@ -0,0 +1,19 @@ +# Correlation against phenotypes fails (for at least some datasets) + +Example: Run a correlation against BXD Published Phenotypes (at the top of the drop-down menu) from here - https://genenetwork.org/show_trait?trait_id=1442370_at&dataset=HC_M2_0606_P + +The bug appears to occur in the rust correlation tool, so I'm not sure how to debug it myself. The last few linnes of the stack trace are as follows: + File "/export2/local/home/zas1024/gn2-zach/gene/wqflask/wqflask/correlation/rust_correlation.py", line 262, in __compute_sample_corr__ + return run_correlation( + File "/usr/local/guix-profiles/gn-latest-20220820/lib/python3.9/site-packages/gn3/computations/rust_correlation.py", line 58, in run_correlation + subprocess.run(command_list, check=True) + File "/gnu/store/qar3sks5fwzm91bl3d3ngyrvxs7ipj5z-python-3.9.9/lib/python3.9/subprocess.py", line 528, in run + raise CalledProcessError(retcode, process.args, +subprocess.CalledProcessError: Command '['/usr/local/guix-profiles/gn-latest-20220820/bin/correlation_rust', '/home/zas1024/gn2-zach/tmp/gn2/correlation/IoaglmTgDJ.json', '/home/zas1024/gn2-zach/tmp/gn2']' died with <Signals.SIGSEGV: 11>. + +## Tags +* assigned: alexm, fredm, zsloan +* type: bug +* keywords: correlations +* status: in-progress +* priority: high |