AlexsLemonade / AlexsLemonade/refinebio

Encountered error in R code while running gene_convert_illumina.R pipeline during processing of /...

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#571 4 comments 0 reactions 0 assignees View on GitHub
backlog zf crunch
Dominant language
Python
Stars
135
Forks
21
PR merge metrics
No merged PRs in 30d

Description

Pretty sure the line with the error message should be using result.returncode and result.stderr. Not e. Assigned myself but if anyone else wants to tackle it before I get to things today, feel free. Should be a quick fix.

https://sentry.io/greenelab/staging-refinebio/issues/667326691/

```
Encountered error in R code while running gene_convert_illumina.R pipeline during processing of /home/user/data_store/GSE98897/raw/GSM2627179-tbl-1.txt.fixed: Can't convert 'NoneType' object to str implicitly
```

Contributor guide

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Research direction

Locate the error-handling code for the gene_convert_illumina.R pipeline and inspect the line that produces the shown message. Verify the available result fields and run the relevant pipeline or tests with a failing R conversion; done means the error reports the command return code and stderr instead of the missing value.

Written by the indexing model from the issue text.

Assessment

Tech stack
python, r
Domain
bioinformatics
Issue type
Bug
Difficulty
2/5
Estimated time
1-3 hours
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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