The bioBakery help forum

Phylophlan3 database in phylophlan command

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
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‘/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

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

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

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

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


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.


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 file to see the command to generate it, reported also below:

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 section of the PhyloPhlAn wiki.


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

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