Running earlier version of GTDB in GTDB-Tk. No such file or directory: '/markers/pfam/individual_hmms/PF01868.17.hmm'

[marialgk]

Even though the last release of GTDB is 202, I need to make an analysis with 95. I have downloaded the database from https://data.gtdb.ecogenomic.org/releases/release95/95.0/auxillary_files/. The downloaded file is indeed 33GB in size, so it seems correct. Long log short, it trows the error:
No such file or directory: '/lustre/database/GTDB-Tk/release95/markers/pfam/individual_hmms/PF01868.17.hmm'
The path is correct. Indeed there is no PF01868.17.hmm, tough other files of the same type exist in the folder.

The complete log:
gtdbtk.log

Environment

• Installed via pip (include the output of pip list)
• Using a conda environment (include the output of conda list && conda list --revisions)
• Using a Docker container (include the IMAGE ID of the container)

(gtdbtk) [marialaura@master taxonomic_classification]$ conda list && conda list --revisions
# packages in environment at /opt/spack/opt/spack/linux-centos7-westmere/gcc-8.2.0/miniconda3-4.7.12.1-slhupgyt5ir7mlt3bfac4pqk623zk4sj/envs/gtdbtk:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       1_gnu    conda-forge
boost                     1.70.0           py38h9de70de_1    conda-forge
boost-cpp                 1.70.0               h7b93d67_3    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
ca-certificates           2021.5.30            ha878542_0    conda-forge
capnproto                 0.6.1                hfc679d8_1    conda-forge
certifi                   2021.5.30        py38h578d9bd_0    conda-forge
dendropy                  4.5.2              pyh3252c3a_0    bioconda
fastani                   1.32                 he1c1bb9_0    bioconda
fasttree                  2.1.10               h779adbc_5    bioconda
gsl                       2.6                  he838d99_2    conda-forge
gtdbtk                    1.5.1              pyhdfd78af_0    bioconda
hmmer                     3.1b2                         3    bioconda
icu                       67.1                 he1b5a44_0    conda-forge
ld_impl_linux-64          2.35.1               hea4e1c9_2    conda-forge
libblas                   3.9.0                9_openblas    conda-forge
libcblas                  3.9.0                9_openblas    conda-forge
libffi                    3.3                  h58526e2_2    conda-forge
libgcc-ng                 9.3.0               h2828fa1_19    conda-forge
libgfortran-ng            9.3.0               hff62375_19    conda-forge
libgfortran5              9.3.0               hff62375_19    conda-forge
libgomp                   9.3.0               h2828fa1_19    conda-forge
liblapack                 3.9.0                9_openblas    conda-forge
libopenblas               0.3.15          pthreads_h8fe5266_1    conda-forge
libstdcxx-ng              9.3.0               h6de172a_19    conda-forge
lz4-c                     1.9.3                h9c3ff4c_0    conda-forge
mash                      2.3                  he348c14_1    bioconda
ncurses                   6.2                  h58526e2_4    conda-forge
numpy                     1.21.0           py38h9894fe3_0    conda-forge
openssl                   1.1.1k               h7f98852_0    conda-forge
pip                       21.1.3             pyhd8ed1ab_0    conda-forge
pplacer                   1.1.alpha19          h9ee0642_2    bioconda
prodigal                  2.6.3                h779adbc_3    bioconda
python                    3.8.10          h49503c6_1_cpython    conda-forge
python_abi                3.8                      2_cp38    conda-forge
readline                  8.1                  h46c0cb4_0    conda-forge
setuptools                49.6.0           py38h578d9bd_3    conda-forge
sqlite                    3.36.0               h9cd32fc_0    conda-forge
tk                        8.6.10               h21135ba_1    conda-forge
tqdm                      4.61.1             pyhd8ed1ab_0    conda-forge
wheel                     0.36.2             pyhd3deb0d_0    conda-forge
xz                        5.2.5                h516909a_1    conda-forge
zlib                      1.2.11            h516909a_1010    conda-forge
zstd                      1.4.9                ha95c52a_0    conda-forge
2021-06-30 14:38:19  (rev 0)
    +_libgcc_mutex-0.1 (conda-forge/linux-64)
    +_openmp_mutex-4.5 (conda-forge/linux-64)
    +boost-1.70.0 (conda-forge/linux-64)
    +boost-cpp-1.70.0 (conda-forge/linux-64)
    +bzip2-1.0.8 (conda-forge/linux-64)
    +ca-certificates-2021.5.30 (conda-forge/linux-64)
    +capnproto-0.6.1 (conda-forge/linux-64)
    +certifi-2021.5.30 (conda-forge/linux-64)
    +dendropy-4.5.2 (bioconda/noarch)
    +fastani-1.32 (bioconda/linux-64)
    +fasttree-2.1.10 (bioconda/linux-64)
    +gsl-2.6 (conda-forge/linux-64)
    +gtdbtk-1.5.1 (bioconda/noarch)
    +hmmer-3.1b2 (bioconda/linux-64)
    +icu-67.1 (conda-forge/linux-64)
    +ld_impl_linux-64-2.35.1 (conda-forge/linux-64)
    +libblas-3.9.0 (conda-forge/linux-64)
    +libcblas-3.9.0 (conda-forge/linux-64)
    +libffi-3.3 (conda-forge/linux-64)
    +libgcc-ng-9.3.0 (conda-forge/linux-64)
    +libgfortran-ng-9.3.0 (conda-forge/linux-64)
    +libgfortran5-9.3.0 (conda-forge/linux-64)
    +libgomp-9.3.0 (conda-forge/linux-64)
    +liblapack-3.9.0 (conda-forge/linux-64)
    +libopenblas-0.3.15 (conda-forge/linux-64)
    +libstdcxx-ng-9.3.0 (conda-forge/linux-64)
    +lz4-c-1.9.3 (conda-forge/linux-64)
    +mash-2.3 (bioconda/linux-64)
    +ncurses-6.2 (conda-forge/linux-64)
    +numpy-1.21.0 (conda-forge/linux-64)
    +openssl-1.1.1k (conda-forge/linux-64)
    +pip-21.1.3 (conda-forge/noarch)
    +pplacer-1.1.alpha19 (bioconda/linux-64)
    +prodigal-2.6.3 (bioconda/linux-64)
    +python-3.8.10 (conda-forge/linux-64)
    +python_abi-3.8 (conda-forge/linux-64)
    +readline-8.1 (conda-forge/linux-64)
    +setuptools-49.6.0 (conda-forge/linux-64)
    +sqlite-3.36.0 (conda-forge/linux-64)
    +tk-8.6.10 (conda-forge/linux-64)
    +tqdm-4.61.1 (conda-forge/noarch)
    +wheel-0.36.2 (conda-forge/noarch)
    +xz-5.2.5 (conda-forge/linux-64)
    +zlib-1.2.11 (conda-forge/linux-64)
    +zstd-1.4.9 (conda-forge/linux-64)

Server information

• RAM: 50GB
• OS: Linux

Debugging information

• gtdbtk.log has been included (drag and drop the file to upload).
• Genomes have been included (if possible, and there are few).

Additional comments

[pchaumeil]

GTDB-Tk v1.5.0+ is not compatible with R05-RS95.
in this version GTDB-Tk uses an updated set of markers not present in R95.

To use R95 data, you need to install/run a previous version of GTDB-Tk (i.e. 1.4.1 )