fastq-dump: command not found, what is wrong?
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2.8 years ago
  1. I have downloaded a tar of SRA toolkit, unzipped and installed it.
  2. I have also done the binary installation where you specify the path and I think I've done it correctly.

Now, I try to use fastq-dump and it runs when I try it out immediately after installation. When I restart terminal and try out fastq-dump, it returns:

fastq-dump: command not found 

What did I do wrong? I've tried the following to see what I did wrong:

  1. I re-run the export path=$path command and fastq-dump still doesn't work.
  2. I re-install SRA toolkit and it works again but doesn't after restarting terminal.
  3. the bin folder is within the SRA toolkit file and it contains the tools.

Can someone point out what I did wrong? Or anything else I forgot to do?

Thank you!

assembly sratoolkit genomics • 6.6k views
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it's not in the path. Try checking the path with echo $PATH

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@OP it is PATH in capital latters, so if you have the binary in e.g. /home/user/foo/bin/ then it is export PATH=$PATH:/home/user/foo/bin/

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Did you do the configuration for sratoolkit?

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6 weeks ago
spalmer • 0

I was having the same problem until I realised I didn't change the version number in the path, I just copy and pasted the path from the instructions, which has the old version number.

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