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Download SRA Data with Singularity

Open jcbioinformatics opened this issue 7 months ago • 0 comments

Hello, I'm having trouble getting Magic-BLAST to pull SRA data when running it with the Singularity image at https://depot.galaxyproject.org/singularity/magicblast:1.7.0--hf1761c0_0

Here's the command that I'm using to test with WSL (Ubuntu 22.04.5 LTS). The genome.fasta file can be downloaded from here

singularity exec magicblast\:1.7.0--hf1761c0_0 magicblast -subject genome.fasta -sra SRR33935013 -out out_TEST.txt

And, that yields the below error.

Error: (2108.2) [magicblast] VDB 3.0.0: 2025-06-12T23:13:33 . sys: encryption failed while validating token within cryptographic module - Verification issue 0x4008 for this certificate: (  cert. version     : 3  serial number     : 00  issuer name       : C=US, O=The Go Daddy Group, Inc., OU=Go Daddy Class 2 Certification Authority  subject name      : C=US, O=The Go Daddy Group, Inc., OU=Go Daddy Class 2 Certification Authority  issued  on        : 2004-06-29 17:06:20  expires on        : 2034-06-29 17:06:20  signed using      : RSA with SHA1  RSA key size      : 2048 bits  basic constraints : CA=true  )
Error: (2108.2) [magicblast] VDB 3.0.0: 2025-06-12T23:13:33 . sys: mbedtls_ssl_get_verify_result for 'locate.ncbi.nlm.nih.gov' returned 0x4008 ( !! The certificate is not correctly signed by the trusted CA  !! The certificate is signed with an unacceptable hash. )
Error: NCBI C++ Exception:
    T0 "/opt/conda/conda-bld/magicblast_1666816348709/work/c++/src/sra/readers/sra/vdbread.cpp", line 869: Error: (CSraException::eOtherError) ncbi::objects::CVDB::CVDB() - Cannot open VDB: SRR33935013 (0x822515ee: connection failed while opening file within cryptographic module)

However, when I run the command below using a conda environment, it works

magicblast -subject genome.fasta -sra SRR33935013 -out out_TEST.txt

I have a very strong preference for using Singularity instead and being able to download from SRA directly, so I'd definitely appreciate any thoughts/advice on resolving this issue

jcbioinformatics avatar Jun 12 '25 23:06 jcbioinformatics