Haha! I ended up doing that itself. Thanks!
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Converting sra to fastq
Hello everyone,
I am trying to convert this set of sra files into the fastq format with the latest version of sratoolkit 2.5.4.1.
But I am getting an error which says the following:
fastq-dump.2.5.2 err: connection busy while validating within network system module - failed ERR375895.sra.
Could anyone please tell me how to resolve this? It would be of great help!
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1 answer
Just get the fastq from EBI: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR375/ERR375895/ERR375895.fastq.gz
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And what is the exact command that you're using?
The command is as follows:
Have you downloaded the SRA file, or are you downloading it on the fly via sra-toolkit? Maybe fastq-dump is trying to download it but has not been properly configured for downloading. Configuring instructions here: https://github.com/ncbi/sra-tools/wiki/Toolkit-Configuration
I have already downloaded the sra file and converting it on the terminal. I am doing this job on a cluster, and when I run the config file, it gives me a system look up error!
Add sratoolkit to environment variables