<p>You have a whitespace here:</p>
<pre><code>e= 40
</code></pre>
<p>awk thinks that 40 is your rule and the rest of the line is a filename.</p>

CC BY-SA 4.0
2021-08-22T09:43:09.003Z
Thank you very much really appreciate it, I didn't notice that. Will give it a try now again.
Justin1609
CC BY-SA 4.0
2021-08-21T15:36:49.883Z
2021-08-21T15:36:49.883Z
Arkadiusz Drabczyk
<p>I am attempting to edit my <code>fastq</code> sequence files with an <code>awk</code> command from a published article. The sequence files are all contained in one directory where I am running the <code>awk</code> command from the terminal in a Linux environment. There are 4 fastq files in the directory</p>
<pre><code>01_thu159_IX_RNA_001.fastq
01_thu163_IX_RNA_001.fastq
01_thu164_IX_RNA_001.fastq
01_thu190_IX_RNA_001.fastq
</code></pre>
<p>I would like to trim all these files at once with the <code>awk</code> command so I wrote this <code>for</code> loop:</p>
<pre><code>for filename in ./*.fastq*
do
awk -v s=10 -v e= 40 ' {if (NR%2 == 0) print substr (<span class="math-container">$0, s+1, length ($</span>0)-s-e); else print <span class="math-container">$0;} ' ./$</span>{filename} &gt;  ./${filename}_trimmed
done
</code></pre>
<p>However, I am getting the following error:</p>
<pre><code>awk: fatal: cannot open file ` {if (NR%2 == 0) print substr (<span class="math-container">$0, s+1, length ($</span>0)-s-e); else print $0;} ' for reading (No such file or directory)
</code></pre>
<p>I then thought maybe it was an error with the <code>for</code> loop so I tried the command as per the instructions in the article</p>
<pre><code>awk -v s=10 -v e= 40 '{if (NR%2 == 0) print substr (<span class="math-container">$0, s+1, length ($</span>0)-s-e); else print $0;}' ./01_thu159_IX_RNA_001.fastq &gt; ./Trim_01_thu159_IX_RNA_001.fastq
</code></pre>
<p>But this also produced the same error:</p>
<pre><code>awk: fatal: cannot open file `{if (NR%2 == 0) print substr (<span class="math-container">$0, s+1, length ($</span>0)-s-e); else print $0;}' for reading (No such file or directory)
</code></pre>
<p>I have checked the syntax for the <code>awk</code> command and it should be correct. Could anyone please give me advice as to what I am doing wrong and how to fix this issue?</p>

<rna-seq><fastq><linux><awk><read-correction>
Error when using awk command to trim sequence files
# Error when using awk command to trim sequence files

(Asked by: username_0 on 2021-08-21)

I am attempting to edit my fastq sequence files with an awk command from a published article. The sequence files are all contained in one directory where I am running the awk command from the terminal in a Linux environment. There are 4 fastq files in the directory
01_thu159_IX_RNA_001.fastq
01_thu163_IX_RNA_001.fastq
01_thu164_IX_RNA_001.fastq
01_thu190_IX_RNA_001.fastq

I would like to trim all these files at once with the awk command so I wrote this for loop:
for filename in ./*.fastq*
do
awk -v s=10 -v e= 40 ' {if (NR%2 == 0) print substr ($0, s+1, length ($0)-s-e); else print $0;} ' ./${filename} >  ./${filename}_trimmed
done

However, I am getting the following error:
awk: fatal: cannot open file ` {if (NR%2 == 0) print substr ($0, s+1, length ($0)-s-e); else print $0;} ' for reading (No such file or directory)

I then thought maybe it was an error with the for loop so I tried the command as per the instructions in the article
awk -v s=10 -v e= 40 '{if (NR%2 == 0) print substr ($0, s+1, length ($0)-s-e); else print $0;}' ./01_thu159_IX_RNA_001.fastq > ./Trim_01_thu159_IX_RNA_001.fastq

But this also produced the same error:
awk: fatal: cannot open file `{if (NR%2 == 0) print substr ($0, s+1, length ($0)-s-e); else print $0;}' for reading (No such file or directory)

I have checked the syntax for the awk command and it should be correct. Could anyone please give me advice as to what I am doing wrong and how to fix this issue?

**Tags:** rna-seq, fastq, linux, awk, read-correction

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## 1 answers

### Answer by username_1 on 2021-08-21. Score: 3

You have a whitespace here:
e= 40

awk thinks that 40 is your rule and the rest of the line is a filename.

> **Comments:**
> **username_0**: Thank you very much really appreciate it, I didn't notice that. Will give it a try now again.  

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