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diffSplice ERROR:__main__:Unknown error: (<class 'UnboundLocalError'>, UnboundLocalError("local variable 'i' referenced before assignment",), <traceback object at 0x7fede986dd48>)
See original GitHub issueIssue Description
Hi I am getting this cryptic error with suppa 2.3. Most of the other splice types are working fine.
suppa.py diffSplice --method empirical --input suppa_results/treated_vs_untreated/AS_events/events_SE_variable_10.ioe --psi suppa_results/treated_vs_untreated/SE_CONTROL.psi suppa_results/treated_vs_untreated/SE_EXPERIMENT.psi --tpm suppa_results/treated_vs_untreated/quantification/CONTROL.tsv suppa_results/treated_vs_untreated/quantification/EXPERIMENT.tsv --area 1000 -gc --lower-bound 0.00 --gene-correction --output Delta_psi_SE --mode DEBUG
Calculating differential analysis between conditions: SE_CONTROL and SE_EXPERIMENT
ERROR:__main__:Unknown error: (<class 'UnboundLocalError'>, UnboundLocalError("local variable 'i' referenced before assignment",), <traceback object at 0x7fede986dd48>)
Here are the relevant files. They should be public: https://debugsuppa.s3.amazonaws.com/CONTROL.tsv https://debugsuppa.s3.amazonaws.com/events_SE_variable_10.ioe https://debugsuppa.s3.amazonaws.com/EXPERIMENT.tsv https://debugsuppa.s3.amazonaws.com/SE_CONTROL.psi https://debugsuppa.s3.amazonaws.com/SE_EXPERIMENT.psi https://debugsuppa.s3.amazonaws.com/iso_tpm_enst.txt
Thanks!
Issue Analytics
- State:
- Created 2 years ago
- Comments:5 (5 by maintainers)
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Thanks for your quick response - you saved me many hours of frustration there. Also thank you for developing SUPPA - it’s wicked fast!
Sorry about the cryptic message.
I tried running the command and reproduced your error.
After a quick look at the files, I saw that there are may nan’s
If you use the option -nan followed by a proportion (e.g. 0.5) it will run.
I tried with -nan 0.5 but only a handful of events were actually computed. You may have to increase the proportion.
I hope this helps
E.
On Fri, 16 Jul 2021 at 22:37, Jeremy Leipzig @.***> wrote:
– Prof. E Eyras EMBL Australia Group Leader The John Curtin School of Medical Research - Australian National University https://github.com/comprna http://scholar.google.com/citations?user=LiojlGoAAAAJ