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
- 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