error in downloading of some accesions with fastq-dump

Question

[pavelasquezv]

Hi all,

When I'm running fastq-dump with some accessions everything works fine, for example:

fastq-dump --split-files SRR10345445 Results are ok

when I am running the program with other access codes I get an error, for example:

fastq-dump --split-files SRR5631167

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 )
2022-06-15T18:43:42 fastq-dump.2.9.6 sys: mbedtls_ssl_get_verify_result returned 0x8 (  !! The certificate is not correctly signed by the trusted CA )
2022-06-15T18:43:42 fastq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '52.217.164.177' from '143.107.211.130'
2022-06-15T18:43:42 fastq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - Failed to create TLS stream for 'sra-pub-run-odp.s3.amazonaws.com' (52.217.164.177) from '143.107.211.130''

This error only happens when I run the program on the server, because from my pc everything works fine.

Please, does anyone know how to fix this problem? I have many sequences to download :(

Many thanks

[lieven.sterck]

sounds like the security certificate handed out by your server is not valid (or at least not signed or recognized).

I think your best option is to contact your server admin and see what you need/can do.

[pavelasquezv]

There are another way to make download of the runs by the server?

[lieven.sterck]

you can try going via ENA?

you can use this webtool to get download links (several ways) : sra-explorer.info

(perhaps you can also get alternative ways to download from SRA)

[pavelasquezv]

Many thanks for you reply. I will try!

Best wishes!

[Utpal]

Hi, could you please let me know how to upgrade sratoolkit in centos? Thanks and regards,

Answer 1

[pavelasquezv]

Hi all,

The problem was solved when I updated the version of the SRA-Toolkit to v3.0. The link dependencies that link up to the cloud storage systems break on older versions of SRA-Toolkit.

I thought it was important to mention

Many thanks

[Guillermo]

Thanks for posting this, I am having the same issue with v2.9.1, so I will check if upgrading to v3.0 will solve this issue.