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fastq-dump: command not found, what is wrong?
  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
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updated by ATpoint ATpoint • written by BioinfoNoob6 • BioinfoNoob6

it's not in the path. Try checking the path with echo $PATH

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written by cpad0112 cpad0112

@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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written by ATpoint ATpoint

Hi, I am having this same problem as OP right now. When I do the echo $PATH command, it returns:

/Users/chachonos/sratoolkit.3.0.0-mac64/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin
chachonos@Caidyns-MacBook-Air ~ %

My SRA toolkit used to work, and so did my terminal, but now most things I put in output this with the various commands I am trying.

zsh: command not found: <command>

I reinstalled the toolkit, which fixed the zsh: command not found error, as the curl did work. However, now, the weird PATH is happening and it keeps outputting

fastq-dump not found

like the OP.

I am very new to bioinformatics and to using terminal in general, so any help would be approeciated.

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written by caidyn.c.j • caidyn.c.j

I'm having this exact same issue. Any insight would be appreciated.

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written by hinilla • hinilla

It's a wrong PATH, as users have commented. If you don't find the command then PATH is wrong or after setting PATH you did not open a new terminal. That's the two possibilities.

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written by ATpoint ATpoint

Did you do the configuration for sratoolkit?

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written by ziziqolo • ziziqolo

1 answer

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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written by spalmer • spalmer

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