Answers.Body: <p>That is a classical problem where the folder containing the binary of the tool is not in PATH, see for example <a href="https://askubuntu.com/questions/109381/how-to-add-path-of-a-program-to-path-environment-variable">https://askubuntu.com/questions/109381/how-to-add-path-of-a-program-to-path-environment-variable</a> or many other threads towards PATH in the SE network.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-03-13T23:22:14.000Z
Answers.Text: Thank you so much @ATpoint
Answers.UserDisplayName: Lucy
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-03-12T08:33:48.343Z
Answers.LastActivityDate: 2024-03-12T08:33:48.343Z
Answers.UserDisplayName: ATpoint
Body: <p>I was able to download all of the SRA files for a specific bioproject using the command:</p>
  <pre><code>prefetch -O output_directory --option-file SRR_Acc_List.txt
  </code></pre>
  <p>I then tried the following command to download those SRA files into FASTQ files:</p>
  <pre><code>find -name \*.sra -exec bsub fastq-dump --split-3 --gzip {} \;
  </code></pre>
  <p>It gave the error:</p>
  <pre><code>find: illegal option -- n
  usage: find [-H | -L | -P] [-EXdsx] [-f path] path ... [expression]
         find [-H | -L | -P] [-EXdsx] -f path [path ...] [expression]
  </code></pre>
  <p>I then tried to add the path:</p>
  <pre><code>find /Users/lucykelly/Desktop/Assel_paper/output_directory -name '*.sra' -exec bsub fastq-dump --split-3 --gzip {} \;
  </code></pre>
  <p>It gave the error:</p>
  <pre><code>find: bsub: No such file or directory
  </code></pre>
  <p>I then tried</p>
  <pre><code>find . -name '*.sra' -exec fasterq-dump --gzip {} \;
  </code></pre>
  <p>and it gave the error:</p>
  <pre><code>find: fasterq-dump: No such file or directory
  </code></pre>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-03-13T03:05:25.880Z
Comments.Text: I agree with @ATPoint. At first I thought it was bsub within the Slurm cluster. If you use `which fasterq-dump` it should throw a blank. The `bsub` error is weird because you should be on the cluster right? Anyway once diagnosed its easy to solve.
Comments.UserDisplayName: M__
Tags: <fastq><sratoolkit><sra><fastq-dump>
Title: Downloading multiple SRA files as FASTQ files using SRA Toolkit
ThreadText: # Downloading multiple SRA files as FASTQ files using SRA Toolkit
  
  (Asked by: username_0 on 2024-03-11)
  
  I was able to download all of the SRA files for a specific bioproject using the command:
  
  ```
  prefetch -O output_directory --option-file SRR_Acc_List.txt
  
  ```
  
  I then tried the following command to download those SRA files into FASTQ files:
  
  ```
  find -name \*.sra -exec bsub fastq-dump --split-3 --gzip {} \;
  
  ```
  
  It gave the error:
  
  ```
  find: illegal option -- n
  usage: find [-H | -L | -P] [-EXdsx] [-f path] path ... [expression]
         find [-H | -L | -P] [-EXdsx] -f path [path ...] [expression]
  
  ```
  
  I then tried to add the path:
  
  ```
  find /Users/lucykelly/Desktop/Assel_paper/output_directory -name '*.sra' -exec bsub fastq-dump --split-3 --gzip {} \;
  
  ```
  
  It gave the error:
  
  ```
  find: bsub: No such file or directory
  
  ```
  
  I then tried
  
  ```
  find . -name '*.sra' -exec fasterq-dump --gzip {} \;
  
  ```
  
  and it gave the error:
  
  ```
  find: fasterq-dump: No such file or directory
  
  ```
  
  **Tags:** fastq, sratoolkit, sra, fastq-dump
  
  > **Comments:**
  > **username_1**: I agree with @ATPoint. At first I thought it was bsub within the Slurm cluster. If you use `which fasterq-dump` it should throw a blank. The `bsub` error is weird because you should be on the cluster right? Anyway once diagnosed its easy to solve.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2024-03-12. Score: 1 | Accepted answer
  
  That is a classical problem where the folder containing the binary of the tool is not in PATH, see for example <https://askubuntu.com/questions/109381/how-to-add-path-of-a-program-to-path-environment-variable> or many other threads towards PATH in the SE network.
  
  > **Comments:**
  > **username_0**: Thank you so much @username_2  
  
  ---
  
  