ERROR when running prepare.py

[Dongxu-Zheng]

Hi, thanks for developing this great software. I am working on a 10X single nucleus RNA-seq data. I use the gtf file from cellRanger as input for the prepare.py. However, I got the ERROR like this:

Traceback (most recent call last):
File "/software/SCAPE/main.py", line 4, in
cli()
File "/software/anaconda3/envs/scape/lib/python3.7/site-packages/click/core.py", line 722, in call
return self.main(*args, **kwargs)
File "/software/anaconda3/envs/scape/lib/python3.7/site-packages/click/core.py", line 697, in main
rv = self.invoke(ctx)
File "/software/anaconda3/envs/scape/lib/python3.7/site-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/software/anaconda3/envs/scape/lib/python3.7/site-packages/click/core.py", line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/software/anaconda3/envs/scape/lib/python3.7/site-packages/click/core.py", line 535, in invoke
return callback(*args, **kwargs)
File "/software/SCAPE/cli/prepare.py", line 83, in prepare
if info[gene_type_id] not in genes_use:
TypeError: unhashable type: 'list'

I installed SCAPE according to the document. The version of Python is 3.7.3. Indeed, I have the output for UTR like:
1 30976 31097 lincRNA;ENSG00000243485;ENST00000473358;MIR1302-2HG . +
1 30976 31109 lincRNA;ENSG00000243485;ENST00000469289;MIR1302-2HG . +
1 34554 35174 lincRNA;ENSG00000237613;ENST00000417324;FAM138A . -
1 35245 35481 lincRNA;ENSG00000237613;ENST00000461467;FAM138A . -

I was wondering if I really need to care about the ERROR and if the output is correct? If you need more info. for my working environment, please let me know. Thanks for any reply and suggestions!

Cheers,
Dongxu

[zhou-ran]

Hi Dongxu,

Try the newest version of scape, https://github.com/chengl7-lab/scape

Ran

[Dongxu-Zheng]

Hi Dongxu,

Try the newest version of scape, https://github.com/chengl7-lab/scape

Ran

Hi Ran, thanks for your reply. I think there is some issues with installing scape visa pip. I got this ERROR:
ERROR: Ignored the following versions that require a different python version: 1.0.0 Requires-Python <3.11,>=3.9; 1.0.1 Requires-Python <3.11,>=3.9; 1.0.2 Requires-Python <3.11,>=3.9
ERROR: Could not find a version that satisfies the requirement scape-apa (from versions: none)
ERROR: No matching distribution found for scape-apa

But I can install it via git successfully and smoothly without any ERROR. I will run the pipeline on my data. Thanks!

Dongxu

[zhou-ran]

Hi Dongxu,

It appears that you've installed scape-apa using Python 3.8; however, the tool requires a minimum Python version of 3.9. Please consider upgrading your Python version accordingly.

You might consider initiating a new issue on that repository, where we can further discuss it.

Ran