I encountered an SSL certificate verification error while running EukCC version 2.1.0 on a CentOS 7 server. The issue occurs when the tool tries to download the NCBI taxonomy database for the first time.
The error traceback suggests an SSL issue with the certificate chain during the urlretrieve call to https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz.md5. The certificate verification failed due to a self-signed certificate in the chain.
I encountered an SSL certificate verification error while running EukCC version 2.1.0 on a CentOS 7 server. The issue occurs when the tool tries to download the NCBI taxonomy database for the first time.
The error traceback suggests an SSL issue with the certificate chain during the urlretrieve call to https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz.md5. The certificate verification failed due to a self-signed certificate in the chain.
Environment: Operating System: CentOS 7 EukCC Version: 2.1.0 Python Version: 3.10 Database Path: `/data/eukccdb/eukcc2_db_ver_1.1
Command Executed:
eukcc single --out eukcc_18sep2024 --threads 12 --db /data/eukccdb/eukcc2_db_ver_1.1 funannotate_29jul2024/TCF417_sorted.fastaError Traceback:ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: self signed certificate in certificate chain (_ssl.c:997)Traceback (most recent call last): File "/usr/local/lib/python3.10/urllib/request.py", line 1348, in do_open h.request(req.get_method(), req.selector, req.data, headers, ... urllib.error.URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: self signed certificate in certificate chain (_ssl.c:997)>Please, let me know how this issue can be resolved in order to run EukCC successfully. Find the log attached. EukCC_Issue_18sep2024.txt