<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>

CC BY-SA 4.0
2024-03-13T23:22:14.000Z
Thank you so much @ATpoint
Lucy
CC BY-SA 4.0
2024-03-12T08:33:48.343Z
2024-03-12T08:33:48.343Z
ATpoint
<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>

CC BY-SA 4.0
2024-03-13T03:05:25.880Z
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.
M__
<fastq><sratoolkit><sra><fastq-dump>
Downloading multiple SRA files as FASTQ files using SRA Toolkit
# 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 @ATpoint  

---

