Download SRA Data with Singularity
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