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harvardinformatics / snpArcher

Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.
MIT License
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KeyError in file #160

Closed weirdo-onlooker closed 3 months ago

weirdo-onlooker commented 3 months ago

Hello, when I was running the program, I temporarily needed to delete a part of the content. I made modifications in config/x.csv, and then encountered this error: KeyError in file /data_32T/yaozc/snpArcher_1/workflow/rules/common.smk, line 31: nan.

File "/data_32T/yaozc/snpArcher_1/workflow/Snakefile", line 63, in File "/data_32T/yaozc/snpArcher_1/workflow/rules/common.smk", line 31, in get_output File "/home/hello/.local/lib/python3.8/site-packages/pandas/core/series.py", line 1007, in getitem File "/home/hello/.local/lib/python3.8/site-packages/pandas/core/series.py", line 1116, in _get_value File "/home/hello/.local/lib/python3.8/site-packages/pandas/core/indexes/multi.py", line 2812, in get_loc File "/home/hello/.local/lib/python3.8/site-packages/pandas/core/indexes/multi.py", line 3187, in _get_level_indexer

How should I handle this?

cademirch commented 3 months ago

Can you share the csv?

weirdo-onlooker commented 3 months ago

PNG_1.txt

weirdo-onlooker commented 3 months ago

I modified the file format because there were garbled characters generated during file transmission due to the presence of Chinese characters.

tsackton commented 3 months ago

It looks like you are missing a BioProject column in your sample sheet. It can be just a random project description (doesn't need to be a real BioProject) but it needs to be present.