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SSL Connection Error with Fastq-dump #808

Closed seanjedi closed 1 year ago

seanjedi commented 1 year ago

Hello, I am new to sra-tools and getting data in general, and I seem to be facing an SSL connection error when trying to use fastq-dump.

I am getting error messages when trying to access data from NCBI, specifically this dataset here: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE226315

This is the error message I get: 2023-04-09T21:59:30 test-sra.2.8.0 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -9984 ( X509 - Certificate verification failed, e.g. CRL, CA or signature check failed ) 2023-04-09T21:59:30 test-sra.2.8.0 sys: mbedtls_ssl_get_verify_result returned 0x8 ( !! The certificate is not correctly signed by the trusted CA )

image

This seems similar to this issue here: https://github.com/ncbi/sra-tools/issues/137

I have tried the steps outlined in the issue above, but it doesn't seem to work for me (IE I tried redownloading Conda, and installing the most recent versions of SRA-tools with no luck)

Any suggestions would be highly appreciated, thank you and have a great day!

klymenko commented 1 year ago

The solution is mentioned. We don't support Conda.

klymenko commented 1 year ago

It looks like you don't run the most recent version of SRA tools after downloading it.

SteffanChristiansen commented 1 year ago

Had the exact same issue. Installed outside conda as suggested and now I can run the test without any issues. You may find this tutorial useful: https://www.youtube.com/watch?v=zE851fWCYQg