fastq- dump error message

Question

[kaelie.nelson]

My first issue is that my laptop is too old for the Rosetta Terminal. I don't think this is a super crucial factor and I can still move forward. When it comes to installing the software, I am repeatedly getting an error message. When I download Biostar information it says the installation is successful but when I enter doctor.py to check if everything was successful

My error message says:

fastq-dump -X 1 -Z SRR1553591
2022-08-02T04:10:58 fastq-dump.2.11.0 sys: mbedtls_ssl_get_verify_result returned 0x8 (  !! The certificate is not correctly signed by the trusted CA  )
Failed to call external services.
(bioinfo)

How can I fix this?

[GenoMax]

The command itself works fine so this appears to be an issue with your install of conda environment? Is this question about material you are following from biostar handbook?

[kaelie.nelson]

I followed all instructions properly or so I thought but I am still getting the error message. Should I uninstall conda environment and try again? How do I go about that?

[ATpoint]

Just enter the accession at sra-explorer.info and get download links for fastq right away:

curl -L ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR155/001/SRR1553591/SRR1553591_1.fastq.gz -o SRR1553591_Zaire_ebolavirus_genome_sequencing_from_2014_outbreak_in_Sierra_Leone_1.fastq.gz
curl -L ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR155/001/SRR1553591/SRR1553591_2.fastq.gz -o SRR1553591_Zaire_ebolavirus_genome_sequencing_from_2014_outbreak_in_Sierra_Leone_2.fastq.gz

No need to fiddle with that terrible ncbi tool.

[Istvan Albert]

To add to the confusion one never knows which tool or approach will perform the job faster. My expectation was always that fastq-dump was always faster but then today I saw the following:

time wget ftp.sra.ebi.ac.uk/vol1/fastq/SRR853/000/SRR8530750/SRR8530750.fastq.gz
real    1m20.171s

vs:

time fasterq-dump --split-3 SRR8530750
real    4m16.036s

vs:

time fastq-dump --split-3 SRR8530750
real    3m51.853s

so fasterq-dump is actually slower than fastq-dump and much slower than directly downloading from across the ocean... Thanks NCBI! (/sarcasm)

All the while downloading a 1GB game via Steam takes less than 30 seconds ...

Answer 1

[Istvan Albert]

See the following:

https://github.com/biostars/biostar-handbook/discussions/200

I have written an installer that downloads and installs the native client distributed by NCBI. I have written a bash shell installer for it. Run:

curl http://data.biostarhandbook.com/sratools.sh | bash

After running the above, close and reopen the terminal, then test the results with:

fastq-dump --stdout -X 2 SRR390728