SRA Toolkit Error while using prefetch
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?
2 answers
Try using SRA explorer to download FASTQ directly. SRA format is a big waste of time.
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colindaven
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.
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What OS are you doing this on? It is best to install
sratoolkitusingcondato avoid these types of problems.