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I am trying to extract data from this: https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR6245218

I installed SRA Toolkit, downloaded the SRR6245218 file and executed this:

fastq-dump -X 5 SRR6245218 --fasta -O ./

The result is a fasta file 900 bytes long, which does not contain the mitochondrial data that I need. What am I doing wrong?

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Your command is fine. It is working as expected. Did you intend to include -X 5 in your command? That restricts the number of spots to 5. If you drop it, you will download the entire set of 2563898 spots.

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  • $\begingroup$ I see. I expected to get mitochondrion DNA. Not sure what I am getting here. But I already found it in fasta format somewhere else. $\endgroup$
    – juanjo75es
    Nov 29 '19 at 16:27

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