humann3 --protein-database database naming requirements are too restrictive

[nick-youngblut]

humann3 (3.0.0.alpha.3) requires that the --protein-database directory only contain the *.dmnd named as it is looking for (eg., uniref90_201901.dmnd). If anything else is in the same directory, humann3 throws an error:

CRITICAL ERROR: The directory provided for the translated database contains files ( XXX ) that are not of the expected version. Please install the latest version of the database: 201901

...which seems completely unnecessary. Also the required file naming (eg., 201901) don't take custom databases into account, which could have other names.

conda info:

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                      1_llvm    conda-forge
bcbio-gff                 0.6.6                      py_0    bioconda
biom-format               2.1.8            py37hc1659b7_0    conda-forge
biopython                 1.77             py37h8f50634_0    conda-forge
blast                     2.9.0                h20b68b9_1    bioconda
boost                     1.68.0          py37h8619c78_1001    conda-forge
boost-cpp                 1.68.0            h11c811c_1000    conda-forge
bowtie2                   2.4.1            py37h4ef193e_2    bioconda
brotlipy                  0.7.0           py37h8f50634_1000    conda-forge
bx-python                 0.8.9            py37h5266303_0    bioconda
bzip2                     1.0.8                h516909a_2    conda-forge
ca-certificates           2020.6.20            hecda079_0    conda-forge
certifi                   2020.6.20        py37hc8dfbb8_0    conda-forge
cffi                      1.14.0           py37hd463f26_0    conda-forge
chardet                   3.0.4           py37hc8dfbb8_1006    conda-forge
click                     7.1.2              pyh9f0ad1d_0    conda-forge
cmseq                     1.0                pyh5ca1d4c_0    bioconda
cryptography              2.9.2            py37hb09aad4_0    conda-forge
cycler                    0.10.0                     py_2    conda-forge
dendropy                  4.4.0                      py_1    bioconda
diamond                   0.9.24               ha888412_1    bioconda
fasttree                  2.1.10               h516909a_4    bioconda
freetype                  2.10.2               he06d7ca_0    conda-forge
future                    0.18.2           py37hc8dfbb8_1    conda-forge
glpk                      4.65              he80fd80_1002    conda-forge
gmp                       6.2.0                he1b5a44_2    conda-forge
gnutls                    3.6.13               h79a8f9a_0    conda-forge
h5py                      2.10.0          nompi_py37h90cd8ad_103    conda-forge
hdf5                      1.10.6          nompi_h3c11f04_100    conda-forge
htslib                    1.10.2               hd3b49d5_1    bioconda
humann                    3.0.0.alpha.3    py37h83b1523_0    biobakery
icu                       58.2              hf484d3e_1000    conda-forge
idna                      2.10               pyh9f0ad1d_0    conda-forge
iqtree                    2.0.3                h176a8bc_0    bioconda
kiwisolver                1.2.0            py37h99015e2_0    conda-forge
krb5                      1.17.1               hfafb76e_1    conda-forge
ld_impl_linux-64          2.34                 h53a641e_5    conda-forge
libblas                   3.8.0               17_openblas    conda-forge
libcblas                  3.8.0               17_openblas    conda-forge
libcurl                   7.71.1               hcdd3856_0    conda-forge
libdeflate                1.6                  h516909a_0    conda-forge
libedit                   3.1.20191231         h46ee950_0    conda-forge
libffi                    3.2.1             he1b5a44_1007    conda-forge
libgcc-ng                 9.2.0                h24d8f2e_2    conda-forge
libgfortran-ng            7.5.0                hdf63c60_6    conda-forge
liblapack                 3.8.0               17_openblas    conda-forge
libopenblas               0.3.10               h5ec1e0e_0    conda-forge
libpng                    1.6.37               hed695b0_1    conda-forge
libssh2                   1.9.0                hab1572f_2    conda-forge
libstdcxx-ng              9.2.0                hdf63c60_2    conda-forge
llvm-openmp               10.0.0               hc9558a2_0    conda-forge
lzo                       2.10              h14c3975_1000    conda-forge
mafft                     7.471                h516909a_0    bioconda
matplotlib-base           3.1.1            py37hfd891ef_0    conda-forge
metaphlan                 3.0.1              pyh5ca1d4c_0    bioconda
muscle                    3.8.1551             hc9558a2_5    bioconda
ncurses                   6.1               hf484d3e_1002    conda-forge
nettle                    3.4.1             h1bed415_1002    conda-forge
numpy                     1.18.5           py37h8960a57_0    conda-forge
openssl                   1.1.1g               h516909a_0    conda-forge
pandas                    1.0.5            py37h0da4684_0    conda-forge
patsy                     0.5.1                      py_0    conda-forge
pcre                      8.44                 he1b5a44_0    conda-forge
perl                      5.26.2            h516909a_1006    conda-forge
perl-archive-tar          2.32                    pl526_0    bioconda
perl-carp                 1.38                    pl526_3    bioconda
perl-common-sense         3.74                    pl526_2    bioconda
perl-compress-raw-bzip2   2.087           pl526he1b5a44_0    bioconda
perl-compress-raw-zlib    2.087           pl526hc9558a2_0    bioconda
perl-exporter             5.72                    pl526_1    bioconda
perl-exporter-tiny        1.002001                pl526_0    bioconda
perl-extutils-makemaker   7.36                    pl526_1    bioconda
perl-io-compress          2.087           pl526he1b5a44_0    bioconda
perl-io-zlib              1.10                    pl526_2    bioconda
perl-json                 4.02                    pl526_0    bioconda
perl-json-xs              2.34            pl526h6bb024c_3    bioconda
perl-list-moreutils       0.428                   pl526_1    bioconda
perl-list-moreutils-xs    0.428                   pl526_0    bioconda
perl-pathtools            3.75            pl526h14c3975_1    bioconda
perl-scalar-list-utils    1.52            pl526h516909a_0    bioconda
perl-types-serialiser     1.0                     pl526_2    bioconda
perl-xsloader             0.24                    pl526_0    bioconda
phylophlan                3.0                        py_5    bioconda
pigz                      2.3.4                hed695b0_1    conda-forge
pip                       20.1.1                     py_1    conda-forge
pycparser                 2.20               pyh9f0ad1d_2    conda-forge
pyopenssl                 19.1.0                     py_1    conda-forge
pyparsing                 2.4.7              pyh9f0ad1d_0    conda-forge
pysam                     0.16.0.1         py37hc501bad_0    bioconda
pysocks                   1.7.1            py37hc8dfbb8_1    conda-forge
python                    3.7.6           cpython_h8356626_6    conda-forge
python-dateutil           2.8.1                      py_0    conda-forge
python-lzo                1.12            py37h81344f2_1001    conda-forge
python_abi                3.7                     1_cp37m    conda-forge
pytz                      2020.1             pyh9f0ad1d_0    conda-forge
raxml                     8.2.12               h516909a_2    bioconda
readline                  8.0                  hf8c457e_0    conda-forge
requests                  2.24.0             pyh9f0ad1d_0    conda-forge
samtools                  1.10                 h9402c20_2    bioconda
scipy                     1.5.0            py37ha3d9a3c_0    conda-forge
seaborn                   0.10.1                        1    conda-forge
seaborn-base              0.10.1                     py_1    conda-forge
seqkit                    0.13.0                        0    bioconda
setuptools                49.1.0           py37hc8dfbb8_0    conda-forge
six                       1.15.0             pyh9f0ad1d_0    conda-forge
sqlite                    3.32.3               hcee41ef_0    conda-forge
statsmodels               0.11.1           py37h8f50634_2    conda-forge
tbb                       2020.1               hc9558a2_0    conda-forge
tk                        8.6.10               hed695b0_0    conda-forge
tornado                   6.0.4            py37h8f50634_1    conda-forge
trimal                    1.4.1                h6bb024c_3    bioconda
urllib3                   1.25.9                     py_0    conda-forge
wheel                     0.34.2                     py_1    conda-forge
xz                        5.2.5                h516909a_0    conda-forge
zlib                      1.2.11            h516909a_1006    conda-forge

[nick-youngblut]

I just wanted to ping this. The current humann3 restrictions hinder the use of custom databases with custom naming. It seems that PRs are generally not being accepted (only 1 of 5 accepted so far, although many are fairly old now), so I feel that I cannot provide a PR that deals with this issue.

[nick-youngblut]

It appears that the newest version of humann3 requires uniref50_201901b.dmnd instead of uniref50_201901.dmnd, so I had to rename my custom diamond database from uniref50_201901.dmnd to uniref50_201901b.dmnd, even though it's the same database.
It would be very helpful if we could just provide the file path (regardless of the file name) instead of using this restrictive formatting.

[github-actions]

Thank you for creating this issue.
We currently field issues through our bioBakery Discourse Support Forum.
If you would please post the issue to discourse we would be happy to sync up with you to get it resolved.

[alienzj]

I meet the same issue.
When I git clone the HUMAnN code (master branch), and test HUMAnN 3.1.0, but it told me:

CRITICAL ERROR: The directory provided for the translated database contains files ( uniref90_demo_prots_v201901b.dmnd ) that are not of the expected version. Please install the latest version of the database: v201901_v31

From humann_databases command, I can't download v201901_v31.
Maybe it is really hard to make code contribution to the biobakery ecosystem.

I also agree with you @nick-youngblut, PRs is hard to be accepted.
For example, I create PR:
#15
#41
#42

[github-actions]

Thank you for creating this issue.
We currently field issues through our bioBakery Discourse Support Forum.
If you would please post the issue to discourse we would be happy to sync up with you to get it resolved.

[github-actions]

Thank you for creating this issue.
We currently field issues through our bioBakery Discourse Support Forum.
If you would please post the issue to discourse we would be happy to sync up with you to get it resolved.