# No error for running MetaPhlAn3, but nothing in the output file - profile.txt

**URL:** <https://forum.biobakery.org/t/no-error-for-running-metaphlan3-but-nothing-in-the-output-file-profile-txt/3241>\
**Category:** MetaPhlAn\
**Created:** [March 1, 2022, 3:50am UTC](https://forum.biobakery.org/t/no-error-for-running-metaphlan3-but-nothing-in-the-output-file-profile-txt/3241 "2022-03-01T03:50:22Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Claire](https://avatars.discourse-cdn.com/v4/letter/c/f6c823/32.png) [@Claire](https://forum.biobakery.org/u/Claire)\
**Post date:** [March 1, 2022, 3:50am UTC](https://forum.biobakery.org/t/no-error-for-running-metaphlan3-but-nothing-in-the-output-file-profile-txt/3241/1 "2022-03-01T03:50:23Z")

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Hi all,

I ran MetaPhlAn3 for one metagenomics sample at the back end with the command:

> `metaphlan sample1.fa --input_type fasta --nproc 30 > sample1_profile.txt`

No error was reported and there were 2 output files. However, **nothing was written to the output file - sample1\_profile.txt**

> -rwxr–r-- 1 claire claire 16507925362 Feb 25 22:39 sample1.fa\*  
> -rw-r–r-- 1 claire claire 134433986 Mar 1 00:30 sample1.fa.bowtie2out.txt  
> **-rw-r–r-- 1 claire claire 0 Mar 1 00:18 sample1\_profile.txt**

According to the nohup.out, there is no error. Strangely, the content inside the nohup.txt seem to be the “real” output for profile.txt.  
[nohup.txt](https://forum.biobakery.org/uploads/short-url/fPxaiLNvkZI7mH5URePhbNj4NYN.txt) (58.3 KB)

 ![image](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/2X/9/92cb68e766c9ee7f44e5b8cfffb8a9b65415daaa.png)

Any comments or suggestions on this issue would be highly appreciated.

Best regards,  
Claire

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<div class="post-metadata">

**Author:** ![Claire](https://avatars.discourse-cdn.com/v4/letter/c/f6c823/32.png) [@Claire](https://forum.biobakery.org/u/Claire)\
**Post date:** [March 2, 2022, 10:01am UTC](https://forum.biobakery.org/t/no-error-for-running-metaphlan3-but-nothing-in-the-output-file-profile-txt/3241/2 "2022-03-02T10:01:22Z")

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Hi @fbeghini ,

Not sure whether I’m tagging the right person. Just wondering you have any idea how to solve the issue?

Best regards,  
Claire

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**Author:** ![aitor.blancomiguez](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/aitor.blancomiguez/32/86_2.png) [@aitor.blancomiguez](https://forum.biobakery.org/u/aitor.blancomiguez)\
**Post date:** [May 27, 2022, 3:00pm UTC](https://forum.biobakery.org/t/no-error-for-running-metaphlan3-but-nothing-in-the-output-file-profile-txt/3241/3 "2022-05-27T15:00:40Z")

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Hi @Claire  
You should be able to solve this problem by using the `-o` parameter instead of `>`  
E.g: `metaphlan sample1.fa --input_type fasta --nproc 30 -o sample1_profile.txt`