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AllenWLynch / lisa

MIT License
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"Data is malformed or incomplete" error for mm10 #1

Closed skannan4 closed 4 years ago

skannan4 commented 4 years ago

Hi! I was trying to run Lisa for a mouse gene list of interest. I used the following line:

lisa oneshot mm10 c1_10.txt -b 3000 -c 1 --seed=2556 > results.tsv

However, this threw the following error: FileNotFoundError: [Errno 2] No such file or directory: '/home/skannan4/anaconda3/envs/lisa_env/lib/python3.8/site-packages/lisa/data/mm10/gene_locs.txt'

As indicated in the error, when I went to the specified folder, the only file was genes.tsv. (By contrast, the hg38 folder was filled with several relevant files - and the oneshot command worked when replacing mm10 with hg38).

I tried lisa download mm10 - this ran with no errors, but finished in maybe under 5 seconds, with no additional files downloaded (by contrast, it took ~20 minutes to download the files associated with hg38).

Is there something I need to do here to get the mouse data?

liulab-dfci commented 4 years ago

Hi Skannan, my testers were exclusively using human genes, so I haven't updated the mm10 data package to the newest version. I will be formatting the data today and it should be available early next week!

liulab-dfci commented 4 years ago

I have completed formatting the mm10 data. You should be able to download it using "lisa download mm10" in your LISA environment.

skannan4 commented 4 years ago

Thanks, it worked! I'll go ahead and close this issue.