<p>This indeed looks like some sort of binary file. I have seen bunch of those when people renamed <code>.fastq.gz</code> to <code>.fastq</code> without actually uncompressing them. However, as you say, this is not your case, as <code>file pair1.fastq</code> would identify the file as <code>gzip compressed data</code>.</p>
<p>Looking at possible return values of <code>file</code> comments <a href="https://unix.stackexchange.com/questions/151008/linux-file-command-classifying-files">here</a>, <code>data</code> basically mean the command could not figure out anything about it beside being some sort of binary data file, but I suspect it probably somehow broken file. Honestly, at this point I think you should check the source of the data. If it's from a public database, re-download the data. If it's your own sequencing, contact the sequencing provider and check the data with them. I don't see any way to rescue this file (which does not necerasrily mean there is nothing you can do).</p>

CC BY-SA 4.0
2021-05-13T13:06:37.947Z
thanks again for the quick response. I was afraid that that might be the case. unfortunately the file came from a collaborator not a public database. I will have to bring that to their attention.
iichelhadi
CC BY-SA 4.0
2021-05-13T13:03:34.673Z
2021-05-13T13:03:34.673Z
Kamil S Jaron
<p>I have paired-end fastq files some of which seem to be in a weird format (from a collaborator, not a public database). When I <code>cat</code> the file I get what seem to me to be binary syntax but not sure?</p>
<p><a href="https://i.sstatic.net/CvKUz.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/CvKUz.png" alt="weird output" /></a></p>
<p>However when I <code>cat</code> into the other pair-end the output seems fine</p>
<p><a href="https://i.sstatic.net/N9ouH.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/N9ouH.png" alt="correct output" /></a></p>
<p>Any help/suggestion/solution would be greatly appreciated.</p>
<p>It does seem to be compressed with a missing suffix:</p>
<pre><code>file pair1.fastq
   pair1.fastq: data.
</code></pre>

CC BY-SA 4.0
2021-05-13T12:52:07.110Z
When I run `file pair1.fastq` on the problem fastq file I get the following output: `pair1.fastq: data`. When I run it on the other pair-end file which doesn't have any issues I get `pair2.fastq: gzip compressed data, extra field`
iichelhadi
CC BY-SA 4.0
2021-05-14T18:14:47.683Z
`gzip compressed data, extra field` is probably produced using `bgzip`. If it were simple `gzip`, the `extra field` part wouldn't be there.
Ram RS
<phylogenetics><ngs><trimming><bowtie2>
fastq file format unknown
# fastq file format unknown

(Asked by: username_0 on 2021-05-13)

I have paired-end fastq files some of which seem to be in a weird format (from a collaborator, not a public database). When I cat the file I get what seem to me to be binary syntax but not sure?

However when I cat into the other pair-end the output seems fine

Any help/suggestion/solution would be greatly appreciated.
It does seem to be compressed with a missing suffix:
file pair1.fastq
   pair1.fastq: data.

**Tags:** phylogenetics, ngs, trimming, bowtie2
> **Comments:**
> **username_0**: When I run `file pair1.fastq` on the problem fastq file I get the following output: `pair1.fastq: data`. When I run it on the other pair-end file which doesn't have any issues I get `pair2.fastq: gzip compressed data, extra field`  
> **username_1**: `gzip compressed data, extra field` is probably produced using `bgzip`. If it were simple `gzip`, the `extra field` part wouldn't be there.  

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## 1 answers

### Answer by username_2 on 2021-05-13. Score: 3

This indeed looks like some sort of binary file. I have seen bunch of those when people renamed `.fastq.gz` to `.fastq` without actually uncompressing them. However, as you say, this is not your case, as `file pair1.fastq` would identify the file as `gzip compressed data`.

Looking at possible return values of `file` comments [here](https://unix.stackexchange.com/questions/151008/linux-file-command-classifying-files), `data` basically mean the command could not figure out anything about it beside being some sort of binary data file, but I suspect it probably somehow broken file. Honestly, at this point I think you should check the source of the data. If it's from a public database, re-download the data. If it's your own sequencing, contact the sequencing provider and check the data with them. I don't see any way to rescue this file (which does not necerasrily mean there is nothing you can do).

> **Comments:**
> **username_0**: thanks again for the quick response. I was afraid that that might be the case. unfortunately the file came from a collaborator not a public database. I will have to bring that to their attention.  

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