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authorFrederick Muriuki Muriithi2022-10-03 07:12:07 +0300
committerFrederick Muriuki Muriithi2022-10-03 07:12:07 +0300
commit3602732e4b133efb670f7821d2b33d99a3b0c1f2 (patch)
treec6ef7443f76fc293f0704e56b38c06fa95888765 /issues
parenta257c7b0ec996964ed1956bedec36cf9f0b34c23 (diff)
downloadgn-gemtext-3602732e4b133efb670f7821d2b33d99a3b0c1f2.tar.gz
Issues (phenotype-correlation-error.gmi): update formatting
Diffstat (limited to 'issues')
-rw-r--r--issues/phenotype-correlation-error.gmi10
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