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author | Frederick Muriuki Muriithi | 2025-05-15 14:32:49 -0500 |
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committer | Pjotr Prins | 2025-06-13 07:00:19 +0200 |
commit | 46079c7b4acea560bb97c8a8a31fc3681fbf211b (patch) | |
tree | d0b6d69f01dd63e769072382306c3e023bdc0343 | |
parent | 5cb6204ad791bc3def39eda331b70b1612ef48dc (diff) | |
download | gn-gemtext-46079c7b4acea560bb97c8a8a31fc3681fbf211b.tar.gz |
GN3: (issues): R/qtl2 mapping error.
-rw-r--r-- | issues/genenetwork3/rqtl2-mapping-error.gmi | 42 |
1 files changed, 42 insertions, 0 deletions
diff --git a/issues/genenetwork3/rqtl2-mapping-error.gmi b/issues/genenetwork3/rqtl2-mapping-error.gmi new file mode 100644 index 0000000..480c7c6 --- /dev/null +++ b/issues/genenetwork3/rqtl2-mapping-error.gmi @@ -0,0 +1,42 @@ +# R/qtl2 Maps Error + +## Tags + +* type: bug +* status: open +* priority: high +* assigned: alexm, zachs, fredm +* keywords: R/qtl2, R/qtl2 Maps, gn3, genetwork3, genenetwork 3 + +## Reproduce + +* Go to https://genenetwork.org/ +* In the "Get Any" field, enter "synap*" and press the "Enter" key +* In the search results, click on the "1435464_at" trait +* Expand the "Mapping Tools" accordion section +* Select the "R/qtl2" option +* Click "Compute" +* In the "Computing the Maps" page that results, click on "Display System Log" + +### Observed + +A traceback is observed, with an error of the following form: + +``` +⋮ +FileNotFoundError: [Errno 2] No such file or directory: '/opt/gn/tmp/gn3-tmpdir/JL9PvKm3OyKk.txt' +``` + +### Expected + +The mapping runs successfully and the results are presented in the form of a mapping chart/graph and a table of values. + +### Debug Notes + +The directory "/opt/gn/tmp/gn3-tmpdir/" exists, and is actually used by other mappings (i.e. The "R/qtl" and "Pair Scan" mappings) successfully. + +This might imply a code issue: Perhaps +* a path is hardcoded, or +* the wrong path value is passed + +The same error occurs on https://cd.genenetwork.org but does not seem to prevent CD from running the mapping to completion. Maybe something is missing on production — what, though? |