fastq-dump - connection failed

Question

[eimanpharmacist]

Hi,

I need to install a specific RNA sequence data using sra toolkit. I installed the toolkit using this command:

sudo apt install sra-toolkit

Then confirmed installation by which fastq-dump

and got this /usr/bin/fastq-dump

But when downloaded SRR21627290 
fastq-dump --stdout -X 2 SRR21627290

I got this error

2023-05-17T23:40:44 fastq-dump.2.8.2 sys: libs/kns/tls.c:930:ktls_handshake: 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 )
2023-05-17T23:40:44 fastq-dump.2.8.2 sys: 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.  )
2023-05-17T23:40:44 fastq-dump.2.8.2 sys: libs/kns/tls.c:930:ktls_handshake: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.29.110'
2023-05-17T23:40:44 fastq-dump.2.8.2 sys: libs/kns/tls.c:930:ktls_handshake: connection failed while opening file within cryptographic module - Failed to create TLS stream for 'www.ncbi.nlm.nih.gov' (130.14.29.110)
2023-05-17T23:40:44 fastq-dump.2.8.2 sys: libs/kns/tls.c:930:ktls_handshake: 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 )
2023-05-17T23:40:44 fastq-dump.2.8.2 sys: 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.  )
2023-05-17T23:40:44 fastq-dump.2.8.2 sys: libs/kns/tls.c:930:ktls_handshake: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.29.110'
2023-05-17T23:40:44 fastq-dump.2.8.2 sys: libs/kns/tls.c:930:ktls_handshake: connection failed while opening file within cryptographic module - Failed to create TLS stream for 'www.ncbi.nlm.nih.gov' (130.14.29.110)
2023-05-17T23:40:45 fastq-dump.2.8.2 sys: libs/kns/tls.c:930:ktls_handshake: 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 )
2023-05-17T23:40:45 fastq-dump.2.8.2 sys: 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.  )
2023-05-17T23:40:45 fastq-dump.2.8.2 sys: libs/kns/tls.c:930:ktls_handshake: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.29.110'
2023-05-17T23:40:45 fastq-dump.2.8.2 sys: libs/kns/tls.c:930:ktls_handshake: connection failed while opening file within cryptographic module - Failed to create TLS stream for 'www.ncbi.nlm.nih.gov' (130.14.29.110)
2023-05-17T23:40:45 fastq-dump.2.8.2 err: libs/vfs/manager.c:1614:VFSManagerOpenDirectoryReadKfs: item not found while constructing within virtual database module - the path 'SRR21627290' cannot be opened as database or table

Any help, please?

Thanks!

[ATpoint]

You can enter the accession on the sra-explorer.info website and get a direct fastq download link. fastq-dump is plain terrible.

Answer 1

[GenoMax]

apt install is probably giving you an old version of sra-toolkit which is likely generating this error.

Get the latest binaries and see if that takes care of the error --> How can I update fastq-dump to 3.0.0?