This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Error: connection failed and certificated verification failed in fastq-dump

I am currently using Ubuntu-18.04 on wsl2. I saved ext4.vhdx on my D: drive and linked the path to it (to solve the problem of data capacity). After that, I tried to use sra-toolkit for 'fastq-dump --stdout -X 2 SRR390728', but I encountered the following error.

wyt@DESKTOP-JP143U9:~$ fastq-dump --stdout -X 2 SRR390728
2023-04-26T08:41:41 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 )
2023-04-26T08:41:41 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.  )
2023-04-26T08:41:41 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'
2023-04-26T08:41:41 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)
2023-04-26T08:41:41 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 )
2023-04-26T08:41:41 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.  )
2023-04-26T08:41:41 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'
2023-04-26T08:41:41 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)
2023-04-26T08:41:42 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 )
2023-04-26T08:41:42 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.  )
2023-04-26T08:41:42 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'
2023-04-26T08:41:42 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)
2023-04-26T08:41:42 fastq-dump.2.8.2 err: libs/vfs/manager.c:1614:VFSManagerOpenDirectoryReadKfs: item not found while constructing within virtual database module - the path 'SRR390728' cannot be opened as database or table

I even tried to follow the instructions on https://www.ncbi.nlm.nih.gov/sra/docs/sra-dbgap-download-old/, but the error still persists. Can you please help me resolve this? For reference, I have also upgraded to version sra-toolkit.3.0.2

sra-toolkit fastq-dump ubuntu
• 4,234 views • link
updated by Istvan Albert Istvan Albert • written by wyt1995 • wyt1995

You can enter the accessions here and get fastq download links directly without the sratoolkit mess.

• 0 views • link
written by ATpoint ATpoint

Thank you for suggesting an alternative solution! I'll try this method if I can't find any other solutions in the future.

• 0 views • link
written by wyt1995 • wyt1995

1 answer

You can use my bio package see more here: https://www.bioinfo.help/

pip install bio

then:

bio search SRR390728

will print a JSON data

[
    {
        "run_accession": "SRR390728",
        "sample_accession": "SAMN00630374",
        "sample_alias": "HS0798",
        "sample_description": "established from ascites of a 45-year-old Caucasian man with diffuse large cell lymphoma",
        "first_public": "2011-12-23",
        "country": "",
        "scientific_name": "Homo sapiens",
        "fastq_bytes": "170346275;168836179",
        "base_count": "516857472",
        "read_count": "7178576",
        "library_name": "HS0798",
        "library_strategy": "RNA-Seq",
        "library_source": "TRANSCRIPTOMIC",
        "library_layout": "PAIRED",
        "instrument_platform": "ILLUMINA",
        "instrument_model": "Illumina Genome Analyzer IIx",
        "study_title": "CGCI: Non-Hodgkin Lymphoma (NHL)",
        "fastq_url": [
            "https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR390/SRR390728/SRR390728_1.fastq.gz",
            "https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR390/SRR390728/SRR390728_2.fastq.gz"
        ],
        "info": "170 MB, 169 MB file; 7 million reads; 516.9 million sequenced bases"
    }
]

you can then get the links to download what you need

• 0 views • link
written by Istvan Albert Istvan Albert

Log in to answer this question.

More posts like this