Question

SRA Toolkit Error while using prefetch

1

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2.5 years ago

Bharat ▴ 10

After installing SRA-toolkit I downloaded an SRA file and when I tried to download another SRA file then it gave me the following error:

prefetch:` symbol lookup error: /lib/x86_64-linux-gnu/libncbi-vdb.so.2: undefined symbol: vdb_mbedtls_md_setup

How to fix this?

sra-toolkit • 3.4k views

ADD COMMENT • link updated 2.5 years ago by GenoMax 141k • written 2.5 years ago by Bharat ▴ 10

0

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What OS are you doing this on? It is best to install sratoolkit using conda to avoid these types of problems.

ADD REPLY • link 2.5 years ago by GenoMax 141k

score 2 · Answer 1 · 2021-10-07

2

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2.5 years ago

colindaven 6.3k

Try using SRA explorer to download FASTQ directly. SRA format is a big waste of time.

https://sra-explorer.info/

ADD COMMENT • link 2.5 years ago by colindaven 6.3k

score 1 · Answer 2 · 2021-10-07

For programmatically downloading fastq files and associated metadata, ENA's API is quite useful. E.g. get links and metadata of fastq files associated to accession PRJNA374918:

curl -X GET "https://www.ebi.ac.uk/ena/portal/api/filereport?accession=PRJNA374918&fields=run_accession,library_name,library_layout,fastq_ftp&result=read_run"

This gives you a sample sheet that you can easily parse to actually download the fastq files.

For fields available to filereport run

curl -X GET "https://www.ebi.ac.uk/ena/portal/api/returnFields?dataPortal=ena&result=read_run"

However, if prefetch gives errors there may be probelms with the accession you are using.