# Phylophlan3 database in phylophlan command

**URL:** <https://forum.biobakery.org/t/phylophlan3-database-in-phylophlan-command/2634>\
**Category:** PhyloPhlAn\
**Created:** [September 23, 2021, 10:48pm UTC](https://forum.biobakery.org/t/phylophlan3-database-in-phylophlan-command/2634 "2021-09-23T22:48:46Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![capfz200](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/capfz200/32/1040_2.png) [@capfz200](https://forum.biobakery.org/u/capfz200)\
**Post date:** [September 23, 2021, 10:48pm UTC](https://forum.biobakery.org/t/phylophlan3-database-in-phylophlan-command/2634/1 "2021-09-23T22:48:47Z")

</div>

Greetings,  
I am trying to build a tree with my mags, but I have problems executing the command phylophlan. In this case, I have the database mags (.fna.gz ) with my mags (.fa) in the same file. The command I am running is:  
phylophlan   
-i ref\_Euryarchaeota   
-t n   
–diversity high   
–accurate   
-f tree\_building\_config.cfg   
–configs\_folder phylophlan\_config\_files   
-o Euryarchaeota\_tree   
-d phylophlan

I have two main errors: the first has to be with the -d phylophlan

1. Command ‘[’/home-1/cperezf2@jhu.edu/.conda/envs/phylophlan3/bin/makeblastdb’, ‘-parse\_seqids’, ‘-dbtype’, ‘nucl’, ‘-in’, ‘phylophlan\_databases/phylophlan/phylophlan.fna’, ‘-out’, ‘phylophlan\_databases/phylophlan/phylophlan’]’ returned non-zero exit status 1.

The second is a bunch of things that I think are related to the conda environment  
2) cannot execute command  
[e] cannot execute command  
command\_line: /home-1/cperezf2@jhu.edu/.conda/envs/phylophlan3/bin/makeblastdb -parse\_seqids -dbtype nucl -in phylophlan\_databases/phylophlan/phylophlan.fna -out phylophlan\_databases/phylophlan/phylophlan  
stdin: None  
stdout: None  
env: {‘LC\_PAPER’: ‘es\_PR.UTF-8’, ‘CPLUS\_INCLUDE\_PATH’: ‘/software/apps/compilers/intel/clck/2018.3/include’, ‘LMOD\_FAMILY\_COMPILER\_VERSION’: ‘18.0’, ‘MARCC\_COMPILER\_MAJOR’: ‘18’, ‘MKLROOT’: ‘/software/apps/compilers/intel/compilers\_and\_libraries\_2018.3.222/linux/mkl’, ‘MANPATH’: ‘/software/apps/mpi/openmpi/3.1/intel/18.0/share/man:/software/apps/compilers/intel/itac/2018.3.022/man:/software/apps/compilers/intel/man/common:/software/apps/compilers/intel/documentation\_2018/en/debugger/gdb-ia/man:/software/apps/compilers/intel/documentation\_2018/en/debugger/gdb-igfx/man:/software/apps/slurm/current/share/man:/software/lmod/lmod/share/man::’, ‘LC\_ADDRESS’: ‘es\_PR.UTF-8’, ‘XDG\_SESSION\_ID’: ‘30891’, ‘LC\_MONETARY’: ‘es\_PR.UTF-8’, ‘HOSTNAME’: ‘bc-login01’, ‘VT\_MPI’: ‘impi4’, ‘_ModuleTable003_’: 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‘/software/lmod/modulefiles/mpi\_compiler/intel/18.0:1;/software/lmod/modulefiles/compiler\_and\_base:1;/software/lmod/modulefiles/apps:1;/software/lmod/modulefiles/holding\_apps:1;/software/lmod/modulefiles/compiled\_apps/intel/18.0:1;/software/lmod/modulefiles/mpi\_compiled\_apps/intel/18.0/openmpi/3.1:1’, ‘CLCK\_ROOT’: ‘/software/apps/compilers/intel/clck/2018.3’, ‘MPI\_INCDIR’: ‘/software/apps/mpi/openmpi/3.1/intel/18.0/include’, ‘HISTSIZE’: ‘1000’, ‘SSH\_CLIENT’: ‘172.16.0.9 44551 22’, ‘LMOD\_SYSTEM\_DEFAULT\_MODULES’: ‘MARCC/summer-2018’, ‘MODULEPATH\_ROOT’: ‘/software/lmod/modulefiles’, ‘GDBSERVER\_MIC’: ‘/software/apps/compilers/intel/debugger\_2018/gdb/targets/intel64/x200/bin/gdbserver’, ‘LMOD\_PACKAGE\_PATH’: ‘/software/lmod/site’, ‘LIBRARY\_PATH’: 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‘LMOD\_sys’: ‘Linux’, ‘PSTLROOT’: ‘/software/apps/compilers/intel/compilers\_and\_libraries\_2018.3.222/linux/pstl’, ‘MARCC\_COMPILER\_MINOR’: ‘0’, ‘CONDA\_EXE’: ‘/software/apps/anaconda/2019.03/bin/conda’, ‘VALGRIND\_LIB’: ‘/software/centos7/lib64/valgrind’, ‘CPATH’: 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‘/software/apps/compilers/intel/clck/2018.3/lib/intel64:1;/software/apps/compilers/intel/compilers\_and\_libraries\_2018.3.222/linux/ipp/lib/intel64:1;/software/apps/compilers/intel/compilers\_and\_libraries\_2018.3.222/linux/compiler/lib/intel64\_lin:1;/software/apps/compilers/intel/compilers\_and\_libraries\_2018.3.222/linux/mkl/lib/intel64\_lin:1;/software/apps/compilers/intel/compilers\_and\_libraries\_2018.3.222/linux/tbb/lib/intel64/gcc4.7:2;/software/apps/compilers/intel/compilers\_and\_libraries\_2018.3.222/linux/daal/lib/intel64\_lin:1;/software/apps/compilers/intel/compilers\_and\_libraries\_2018.3.222/linux/daal/…/tbb/lib/intel64\_lin/gcc4.4:1;/software/centos7/lib64:1;/software/centos7/lib:1;/software/centos7/usr/lib64:1;/software/centos7/usr/lib:1;/software/apps/slurm/current/lib/slurm:1;/software/apps/slurm/current/lib:1’, ‘LESSOPEN’: ‘||/usr/bin/lesspipe.sh %s’, ‘LMOD\_SETTARG\_FULL\_SUPPORT’: ‘no’, ‘\_\_LMOD\_REF\_COUNT\_LD\_LIBRARY\_PATH’: ‘/software/apps/mpi/openmpi/3.1/intel/18.0/lib:1;/software/apps/compilers/intel/itac/2018.3.022/intel64/slib:1;/software/apps/compilers/intel/compilers\_and\_libraries\_2018.3.222/linux/compiler/lib/intel64:1;/software/apps/compilers/intel/compilers\_and\_libraries\_2018.3.222/linux/compiler/lib/intel64\_lin:2;/software/apps/compilers/intel/compilers\_and\_libraries\_2018.3.222/linux/ipp/lib/intel64:1;/software/apps/compilers/intel/compilers\_and\_libraries\_2018.3.222/linux/mkl/lib/intel64\_lin:1;/software/apps/compilers/intel/compilers\_and\_libraries\_2018.3.222/linux/tbb/lib/intel64/gcc4.7:2;/software/apps/compilers/intel/debugger\_2018/iga/lib:1;/software/apps/compilers/intel/debugger\_2018/libipt/intel64/lib:1;/software/apps/compilers/intel/compilers\_and\_libraries\_2018.3.222/linux/daal/lib/intel64\_lin:1;/software/apps/compilers/intel/compilers\_and\_libraries\_2018.3.222/linux/daal/…/tbb/lib/intel64\_lin/gcc4.4:1;/usr/lib:1;/usr/lib64:1;/software/centos7/lib64:1;/software/centos7/lib:1;/software/centos7/usr/lib64:1;/software/centos7/usr/lib:1;/software/apps/slurm/current/lib/slurm:2;/software/apps/slurm/current/lib:2’, ‘PKG\_CONFIG\_PATH’: ‘/software/apps/compilers/intel/compilers\_and\_libraries\_2018.3.222/linux/mkl/bin/pkgconfig:/software/centos7/usr/share/pkgconfig:/software/centos7/usr/lib64/pkgconfig’, ‘CONDA\_DEFAULT\_ENV’: ‘phylophlan3’, ‘INFOPATH’: ‘/software/apps/compilers/intel/documentation\_2018/en/debugger//gdb-ia/info/:/software/apps/compilers/intel/documentation\_2018/en/debugger//gdb-igfx/info/’, ‘LMOD\_FAMILY\_COMPILER’: ‘intel’, ‘DISPLAY’: ‘172.16.5.3:38.0’, ‘XDG\_RUNTIME\_DIR’: ‘/run/user/4426’, ‘CC’: ‘icc’, ‘\_\_LMOD\_REF\_COUNT\_PKG\_CONFIG\_PATH’: ‘/software/apps/compilers/intel/compilers\_and\_libraries\_2018.3.222/linux/mkl/bin/pkgconfig:1;/software/centos7/usr/share/pkgconfig:1;/software/centos7/usr/lib64/pkgconfig:1’, ‘LMOD\_DIR’: ‘/software/lmod/lmod/libexec’, ‘\_\_LMOD\_REF\_COUNT\_MANPATH’: ‘/software/apps/mpi/openmpi/3.1/intel/18.0/share/man:1;/software/apps/compilers/intel/itac/2018.3.022/man:1;/software/apps/compilers/intel/man/common:1;/software/apps/compilers/intel/documentation\_2018/en/debugger/gdb-ia/man:1;/software/apps/compilers/intel/documentation\_2018/en/debugger/gdb-igfx/man:1;/software/apps/slurm/current/share/man:1;/software/lmod/lmod/share/man:1’, ‘LC\_TIME’: ‘es\_PR.UTF-8’, ‘LMOD\_FAMILY\_MPI’: ‘openmpi’, ‘LC\_NAME’: ‘es\_PR.UTF-8’, ‘BASH\_FUNC\_module()’: ‘() { eval $($LMOD\_CMD bash “$@”) && eval $(${LMOD\_SETTARG\_CMD:-:} -s sh)\n}’, ‘BASH\_FUNC\_ml()’: ‘() { eval $($LMOD\_DIR/ml\_cmd “$@”)\n}’}

I am not sure how to solve both problems. Thanks for the help!

Cesar

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<div class="post-metadata">

**Author:** ![f.asnicar](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/f.asnicar/32/196_2.png) [@f.asnicar](https://forum.biobakery.org/u/f.asnicar)\
**Post date:** [September 24, 2021, 9:14pm UTC](https://forum.biobakery.org/t/phylophlan3-database-in-phylophlan-command/2634/2 "2021-09-24T21:14:44Z")

</div>

Dear Cesar, thank you for reporting this.  
The two errors you mentioned seems actually to be the same problem and it is because you are using a configuration file for a nucleotide database while using an amino acid database. The phylophlan database is a set of proteins, so you should use a configuration file to index a protein database and to perform the right mappings. Among the 4 standard configuration files, the supermatrix\_aa.cfg should work.  
Many thanks, Francesco

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<div class="post-metadata">

**Author:** ![capfz200](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/capfz200/32/1040_2.png) [@capfz200](https://forum.biobakery.org/u/capfz200)\
**Post date:** [September 27, 2021, 9:18pm UTC](https://forum.biobakery.org/t/phylophlan3-database-in-phylophlan-command/2634/3 "2021-09-27T21:18:28Z")

</div>

Dear Francesco,  
Thanks for the response. My Mags are nucleotide sequences and the retrived genomes are also nucleotides. I wonder how can I change the -d phylophlan to work with nucleotides or am I missing something?

I also run this command to have my tree\_building\_config.cfg  
phylophlan\_write\_config\_file -o tree\_building\_config.cfg -d n --db\_dna makeblastdb --map\_dna blastn --msa muscle --trim trimal --tree1 fasttree --tree2 raxml

Cesar

---

<div class="post-metadata">

**Author:** ![capfz200](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/capfz200/32/1040_2.png) [@capfz200](https://forum.biobakery.org/u/capfz200)\
**Post date:** [September 27, 2021, 9:42pm UTC](https://forum.biobakery.org/t/phylophlan3-database-in-phylophlan-command/2634/4 "2021-09-27T21:42:38Z")

</div>

I just see that the phylophlan.fna in phylophlan\_databases/phylophlan is empty.

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<div class="post-metadata">

**Author:** ![f.asnicar](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/f.asnicar/32/196_2.png) [@f.asnicar](https://forum.biobakery.org/u/f.asnicar)\
**Post date:** [September 28, 2021, 1:02pm UTC](https://forum.biobakery.org/t/phylophlan3-database-in-phylophlan-command/2634/5 "2021-09-28T13:02:43Z")

</div>

Dear Cesar,  
I’ll reply below quoting the parts from your messages from above.

* * *

> [@capfz200](#):
>
> My Mags are nucleotide sequences and the retrived genomes are also nucleotides. I wonder how can I change the -d phylophlan to work with nucleotides or am I missing something?

This is not a problem, you just need to have the translated search in the mapping file to be able to map your genomes and MAGs against the proteins in the `phylophlan` database.

* * *

> [@capfz200](#):
>
> I also run this command to have my tree\_building\_config.cfg  
> phylophlan\_write\_config\_file -o tree\_building\_config.cfg -d n --db\_dna makeblastdb --map\_dna blastn --msa muscle --trim trimal --tree1 fasttree --tree2 raxml

With the above command, you’re specifying that the database to be used with this config file is a nucleotide one (`-d n`) and you’ll use the `makeblastdb` to index it. If you are using the `phylophlan` database this won’t work and `makeblastdb` will return an error because it will find amino acids instead of nucleotides. You can use the `supermatrix_aa.cfg` that was generated when you installed PhyloPhlAn, or you can have a look at the [`phylophlan_write_default_configs.sh`](https://github.com/biobakery/phylophlan/blob/dfee9606e13589ea579634e847ec9c1e5f35a6b8/phylophlan/phylophlan_write_default_configs.sh) file to see the command to generate it, reported also below:

```Bash
phylophlan_write_config_file -o supermatrix_aa.cfg \
    -d a \
    --db_aa diamond \
    --map_dna diamond \
    --map_aa diamond \
    --msa mafft \
    --trim trimal \
    --tree1 fasttree \
    --tree2 raxml \
    --overwrite \
    --verbose

```

For the above two parts, you can have a look at the [Configuration File](https://github.com/biobakery/phylophlan/wiki#configuration-file) section of the PhyloPhlAn wiki.

* * *

> [@capfz200](#):
>
> I just see that the phylophlan.fna in phylophlan\_databases/phylophlan is empty.

This is strange. Can you please remove the `phylophlan` folder from there and re-run PhyloPhlAn so that the database will be re-downloaded?

Many thanks,  
Francesco

---

<div class="post-metadata">

**Author:** ![capfz200](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/capfz200/32/1040_2.png) [@capfz200](https://forum.biobakery.org/u/capfz200)\
**Post date:** [September 29, 2021, 9:28pm UTC](https://forum.biobakery.org/t/phylophlan3-database-in-phylophlan-command/2634/6 "2021-09-29T21:28:39Z")

</div>

Dear Francesco

I was having some troubles with the cloud computing since they have hardware problems during recent weeks. Maybe that could be a reason since some works were being interrupted from time to time. I will come back to you in a few days when the hardware will be better.

Thanks for all the patience, it was very helpful