diff options
| -rw-r--r-- | issues/phenotype-correlation-error.gmi | 10 |
1 files changed, 8 insertions, 2 deletions
diff --git a/issues/phenotype-correlation-error.gmi b/issues/phenotype-correlation-error.gmi index 1d5fe23..5d034c5 100644 --- a/issues/phenotype-correlation-error.gmi +++ b/issues/phenotype-correlation-error.gmi @@ -1,8 +1,13 @@ -# Correlation against phenotypes fails (for at least some datasets) +# Phenotype Correlation Error -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 +## 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 @@ -10,6 +15,7 @@ The bug appears to occur in the rust correlation tool, so I'm not sure how to de 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 |