# No output files after classify.seqs

**URL:** <https://forum.mothur.org/t/no-output-files-after-classify-seqs/2258>\
**Category:** Commands in mothur\
**Created:** [February 18, 2015, 10:28am UTC](https://forum.mothur.org/t/no-output-files-after-classify-seqs/2258 "2015-02-18T10:28:24Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Anneleen](https://avatars.discourse-cdn.com/v4/letter/a/50afbb/32.png) [@Anneleen](https://forum.mothur.org/u/Anneleen)\
**Post date:** [February 18, 2015, 10:28am UTC](https://forum.mothur.org/t/no-output-files-after-classify-seqs/2258/1 "2015-02-18T10:28:24Z")

</div>

Hi,

I’ve recently downloaded Mothur v.1.34.0 and encountered a problem with classify.seqs command.  
Normally the classify.seqs command gives 2 output files, named \*.taxonomy and \*.tax.summary.

However this is my output …

> mothur \> classify.seqs(fasta=current, count=current, reference=db.fasta, taxonomy=db.tax, cutoff=80, processors=4)  
> Using 1.uchime.pick.count\_table as input file for the count parameter.  
> Using 1.fasta as input file for the fasta parameter.

> Using 4 processors.  
> Generating search database… DONE.  
> It took 3 seconds generate search database.

> Reading in the db.tax taxonomy… HM108361.1.1446 has an error in the taxonomy. This may be due to a ;;  
> DONE.  
> AB000389.1 is in your taxonomy file and is not in your template file. Please correct.  
> AB001518.1 is in your taxonomy file and is not in your template file. Please correct.  
> …  
> Z96096.1 is in your taxonomy file and is not in your template file. Please correct.  
> Z99997.1 is in your taxonomy file and is not in your template file. Please correct.  
> DONE.  
> It took 4 seconds get probabilities.

As you can see, no output files are generated.

Is there an incompatibility with the new Mothur v.1.34.0 or am I overlooking something?

Kind regards,  
Anneleen

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<div class="post-metadata">

**Author:** ![westcott](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/westcott/32/18_2.png) [@westcott](https://forum.mothur.org/u/westcott)\
**Post date:** [February 18, 2015, 2:33pm UTC](https://forum.mothur.org/t/no-output-files-after-classify-seqs/2258/2 "2015-02-18T14:33:15Z")

</div>

Generally errors like this are related to a formatting issue in the taxonomy file. You can see what mothur is reading by using the debug flag.

mothur \> set.dir(debug=t)  
mothur \> classify.seqs(…)

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<div class="post-metadata">

**Author:** ![Anneleen](https://avatars.discourse-cdn.com/v4/letter/a/50afbb/32.png) [@Anneleen](https://forum.mothur.org/u/Anneleen)\
**Post date:** [February 18, 2015, 3:27pm UTC](https://forum.mothur.org/t/no-output-files-after-classify-seqs/2258/3 "2015-02-18T15:27:49Z")

</div>

After loading this into mothur

mothur \> set.dir(debug=t)  
mothur \> classify.seqs(…)

I get the following

> mothur \> set.dir(debug=t)  
> Setting [DEBUG] flag.

> mothur \> classify.seqs(fasta=x.fasta, count=x.count\_table, reference=db.fasta, taxonomy=db.tax, cutoff=80, processors=4)

> Using 4 processors.  
> Generating search database… DONE.  
> It took 6 seconds generate search database.  
> unknown unknown

> Reading in the db.tax taxonomy… [DEBUG]: Taxonomies read in…  
> [DEBUG]: name = ‘AB000389.1’ tax = ‘Bacteria;Proteobacteria;Gammaproteobacteria;Alteromonadales;Pseudoalteromonadaceae;Pseudoalteromonas;’  
> [DEBUG]: name = ‘AB000699.1’ tax = ‘Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae;Nitrosomonas;’  
> …  
> Z96096.1 is in your taxonomy file and is not in your template file. Please correct.  
> Z99997.1 is in your taxonomy file and is not in your template file. Please correct.  
> [DEBUG]: about to generateWordPairDiffArr  
> [DEBUG]: done generateWordPairDiffArr  
> DONE.  
> It took 11 seconds get probabilities.

The debug flag worked fine, but did not give me any output data files after the classify.seqs command.  
But a .tree.sum and .8mer are generated (as I’ve observed before).

Any other solutions?

Kind regards,  
Anneleen