fastq-dump.2.9.0 sys: connection failed

[chen1i6c04]

Hello:

I wanted to download some SRA file with fastq-dump. When running the command fastq-dump --split-files SRR7062492

I receive the following error:

2018-07-04T08:45:49 fastq-dump.2.9.0 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 )
2018-07-04T08:45:49 fastq-dump.2.9.0 sys: mbedtls_ssl_get_verify_result returned 0x14008 (  !! The certificate is not correctly signed by the trusted CA  !! The certificate is signed with an unacceptable hash.  !! The certificate is signed with an unacceptable key (eg bad curve, RSA too short).  )
2018-07-04T08:45:49 fastq-dump.2.9.0 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.27' from '192.168.30.240'
2018-07-04T08:45:49 fastq-dump.2.9.0 sys: connection failed while opening file within cryptographic module - Failed to create TLS stream for 'sra-download.ncbi.nlm.nih.gov' (130.14.250.27) from '192.168.30.240'
2018-07-04T08:45:49 fastq-dump.2.9.0 err: connection failed while opening file within cryptographic module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/traces/sra62/SRR/006896/SRR7062492'
2018-07-04T08:45:49 fastq-dump.2.9.0 err: item not found while constructing within virtual database module - the path 'SRR7062492' cannot be opened as database or table

Somtimes it could run ,but it could not in most of the time. Although I can download file by browser,but it's too trouble. Do you have any idea?

[kwrodarmer]

This error happens when you are victim of a man-in-the-middle attack, or something that looks like it. Our software detects this problem when a browser is more easily fooled.

Sometimes this situation occurs legitimately when your organization is running deep packet inspection firewalls, so while this may not be an actual attack, it looks the same from the client software perspective.

I suggest that you run the command test-sra SRR7062492 and send the output to sra-tools@ncbi.nlm.nih.gov (do NOT post it here) and we can help you to address the issue.

[chen1i6c04]

The program can work after modifying setting of firewall . Thanks your help

[Dhohadh]

Hello everyone, I also try to download SRA files and when I try to test whether the toolbox is functional or not, I still have these messages:

fastq-dump.3.0.0 warn: connection unexpected while executing query within virtual file system module - can’t open NC_000001.11 as a RefSeq or as a WGS 2022-08-26T04:41:23 fastq-dump.3.0.0 err: connection unexpected while executing query within virtual file system module - failed SRR19653847

Does someone have any suggestions or solutions? Thank you.

[PC2021]

What have you done to fix the problem?

[klymenko]

Use a recent toolkit.

[johnne]

I'm also having this issue, on both the most recent and all the older versions from conda that I've tried. The error message I get is:

mbedtls_ssl_get_verify_result returned 0x4008 ( !! The certificate is not correctly signed by the trusted CA !! The certificate is signed with an unacceptable hash. )

The only fix I've found so far is to first create a conda environment, then download the binaries from your repo, extracting and copying into the $CONDA_PREFIX/bin/ directory.

[bozbezbozzel]

I also encountered this problem with conda-- had my base environment on while installing. I did a complete uninstall, deactivated the base env, reinstalled and that worked.