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abyzovlab / CNVpytor

a python extension of CNVnator -- a tool for CNV analysis from depth-of-coverage by mapped reads
MIT License
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rest.ensembl.org connect error #218

Closed jeffchen2000 closed 3 months ago

jeffchen2000 commented 3 months ago

hi

I got rest.ensembl.org connect error, not sure why this step is needed. I believe this error is coming after our IT increasing our server security and disabled outside connection, but is there any way that I can get around of it?

thanks Jeff C

Traceback (most recent call last): File "/miniconda3/lib/python3.11/site-packages/requests/adapters.py", line 486, in send resp = conn.urlopen( ^^^^^^^^^^^^^ File "/miniconda3/lib/python3.11/site-packages/urllib3/connectionpool.py", line 845, in urlopen retries = retries.increment( ^^^^^^^^^^^^^^^^^^ File "/miniconda3/lib/python3.11/site-packages/urllib3/util/retry.py", line 515, in increment raise MaxRetryError(_pool, url, reason) from reason # type: ignore[arg-type] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='rest.ensembl.org', port=443): Max retries exceeded with url: /overlap/region/human/chr1:120200001-121000000?content-type=application/json;feature=gene; (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x154e428464d0>: Failed to establish a new connection: [Errno 101] Network is unreachable'))

arpanda commented 3 months ago

I think, you have enabled the set annotate option, which identifies genes overlapping a CNV region using Ensembl. This is an optional step and can be performed separately as well.

You can either skip the set annotate part or run unset annotate to disable it.

Thank you, Arijit

jeffchen2000 commented 3 months ago

Hi Arijit thanks for quick response. yes, I used "set annotation". but we have large number of samples, I have previously processed most of them with "set annotation". if I skip annotation with these samples and annotate them later, how can I ensure the annotation (reference used etc.) will be the same.

arpanda commented 3 months ago

How did you save your results ? Usually, the set annotation adds columns for genes names overlapping a CNV region. One can take those CNV region and find the overlapping genes.

Otherwise, the reference genome is already stored in the pytor file, it can be used later as well.