follow these steps:

1. Verify Installation: First, ensure that you have installed the required software. The "fastq-dump" tool is part of the SRA Toolkit, which is used to retrieve data from the Sequence Read Archive (SRA) maintained by the National Center for Biotechnology Information (NCBI). Make sure you have installed the SRA Toolkit correctly by following the installation instructions provided by NCBI.

2. Check PATH Variable: Once the SRA Toolkit is installed, check if the directory containing the "fastq-dump" executable is added to your system's PATH variable. The PATH variable is a list of directories that the terminal searches when looking for executable files. To check the PATH variable, open a terminal and run the following command:

```shell

echo $PATH

```

This command will display a colon-separated list of directories. Check if the directory containing the "fastq-dump" executable is included in this list. If it's not, you will need to add it.

3. Add to PATH: If the directory containing the "fastq-dump" executable is not in the PATH variable, you can add it by modifying your shell's configuration file. The specific file you need to modify depends on the shell you are using (e.g., Bash, Zsh, etc.). For example, if you are using Bash, you can edit the `~/.bashrc` file by running the following command:

```shell

nano ~/.bashrc

```

In the file, add the following line at the end:

```shell

export PATH="/path/to/fastq-dump:$PATH"

```

Replace "/path/to/fastq-dump" with the actual path to the directory containing the "fastq-dump" executable.

Save the file and exit the text editor. Then, to apply the changes, either restart your terminal or run the following command:

```shell

source ~/.bashrc

```

4. Verify the Installation: After adding the directory to the PATH variable, open a new terminal and run the following command to verify if the "fastq-dump" command is now recognized:

```shell

fastq-dump --version

```

If everything is set up correctly, this command should display the version of the "fastq-dump" tool installed on your system.

Good luck

If you are encountering the "fastq-dump command not found" error when opening the terminal, it suggests that the fastq-dump command is not recognized as a valid command in your terminal session. This typically happens when the command is not in your system's PATH or when the software that provides the fastq-dump command is not installed or configured correctly.

Here are steps to resolve the issue:

By following these steps, you should be able to resolve the "fastq-dump command not found" error and use the fastq-dump command successfully in your terminal.

I encountered the same error even though I followed all the steps mentioned in the installation document. This issue can be easily resolved by running the following command in the folder where you have extracted the sra-toolkit zip file:

export PATH=$PATH:$PWD/sratoolkit.-/bin

The functionality will be restored.