/mpwt/pwt_wrapper.py: ['Error', 'fatal error', 'No protein-coding genes with sequence data found.', 'Cannot continue.']

[Alexander20mc]

Hi, I have been trying to execute the software metage2metabo, using the command recon which uses pathway tools. I have the following error message:

****lib/python3.9/site-packages/mpwt/pwt_wrapper.py: load_errors = ['Error', 'fatal error', 'No protein-coding genes with sequence data found.', 'Cannot continue.']

I downloaded the NCBI protein database and set the ".ncbirc" file this way:

[ncbi]
/misc/scratch3/rogerlab_databases/other_dbs/blast_protein_database/

the whole error message:

###############################################

Metabolic network reconstruction

###############################################

######### Running metabolic network reconstruction with Pathway Tools #########
---------- Launching mpwt ----------
Check and delete unfinished builds of Pathway Tools.
! PGDB GCA_003433675 already in ptools-local, no PathoLogic inference will be launched on this species.
! PGDB GCA_003433665 already in ptools-local, no PathoLogic inference will be launched on this species.
|Input Check|GCA_003433665| No missing files
|Flat files creation|GCA_003433665| pathway-tools -no-patch-download -disable-metadata-saving -nologfile -load /misc/scratch3/collazos/m2m/workflow_genomes/GCA_003433665/flat_files_creation.lisp
=== Error in flat_files_creation.log for /misc/scratch3/collazos/m2m/workflow_genomes/GCA_003433665===
      Error from the flat_files_creation.log file: /misc/scratch3/collazos/m2m/workflow_genomes/GCA_003433665/flat_files_creation.log
      No protein-coding genes with sequence data found. Cannot continue.

------------////----------------
!!!!!!!!!!!!!!!!!-------------------- End error message for GCA_003433675 --------------------!!!!!!!!!!!!!!!!!
|Output Check|/misc/scratch3/collazos/m2m/workflow_genomes/GCA_003433675| 18 out of 23 dat files created.
|Output Check| WARNING: No pathologic.log file for /misc/scratch3/collazos/m2m/workflow_genomes/GCA_003433665, could not write log.
|Output Check| WARNING: No pathologic.log file for /misc/scratch3/collazos/m2m/workflow_genomes/GCA_003433675, could not write log.
-------------- Checking mpwt runs --------------
/!\ 2 failed runs on a total of 2 runs.
/!\ Error in GCA_003433665 during Moving output files step.
/!\ Error in GCA_003433675 during Moving output files step.
-------------- mpwt has finished in 9.06s! Thank you for using it. --------------
Something went wrong running Pathway Tools. See the log file in /misc/scratch3/collazos/m2m/recon_results4/pgdb_log/log_error.txt

[ArnaudBelcour]

Hi @Alexander20mc,

It is strange because this error occurs when no proteins are found in the genome but they are present in the test files of Metage2Metabo.

Which version of Pathway Tools, mpwt and Metage2Metabo are you using?

Best regards,
Arnaud Belcour.

[Alexander20mc]

Hi @ArnaudBelcour ,

Thank you so much for your reply. I'm working on HPC cluster.......I'm not the person in charge of the system. I'm attaching all packages in the M2M's environment.

for m2m, the latest version was installed (1.61), for mpwt the version is 0.86. and for pathway tools I found 22.5 and 23.0 versions installed

Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
annotated-types 0.6.0 pypi_0 pypi
anyio 4.3.0 pypi_0 pypi
appdirs 1.4.4 pypi_0 pypi
argcomplete 3.2.3 pypi_0 pypi
argh 0.31.2 pypi_0 pypi
arpeggio 2.0.2 pypi_0 pypi
biopython 1.83 pypi_0 pypi
blast 2.15.0 pl5321h6f7f691_1 bioconda
bubbletools 0.6.11 pypi_0 pypi
bzip2 1.0.8 hd590300_5 conda-forge
c-ares 1.28.1 hd590300_0 conda-forge
ca-certificates 2024.2.2 hbcca054_0 conda-forge
certifi 2024.2.2 pypi_0 pypi
cffi 1.16.0 pypi_0 pypi
chardet 5.2.0 pypi_0 pypi
clingo 5.7.1 pypi_0 pypi
clyngor 0.4.3 pypi_0 pypi
clyngor-with-clingo 5.3.post1 pypi_0 pypi
cobra 0.29.0 pypi_0 pypi
curl 8.7.1 hca28451_0 conda-forge
depinfo 2.2.0 pypi_0 pypi
diskcache 5.6.3 pypi_0 pypi
docopt 0.6.2 pypi_0 pypi
entrez-direct 21.6 he881be0_0 bioconda
ete3 3.1.3 pypi_0 pypi
exceptiongroup 1.2.0 pypi_0 pypi
future 1.0.0 pypi_0 pypi
gettext 0.22.5 h59595ed_2 conda-forge
gettext-tools 0.22.5 h59595ed_2 conda-forge
gffutils 0.12 pypi_0 pypi
h11 0.14.0 pypi_0 pypi
httpcore 1.0.5 pypi_0 pypi
httpx 0.27.0 pypi_0 pypi
idna 3.7 pypi_0 pypi
importlib-metadata 7.1.0 pypi_0 pypi
importlib-resources 6.4.0 pypi_0 pypi
iniconfig 2.0.0 pypi_0 pypi
keyutils 1.6.1 h166bdaf_0 conda-forge
krb5 1.21.2 h659d440_0 conda-forge
ld_impl_linux-64 2.40 h41732ed_0 conda-forge
libasprintf 0.22.5 h661eb56_2 conda-forge
libasprintf-devel 0.22.5 h661eb56_2 conda-forge
libcurl 8.7.1 hca28451_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 hd590300_2 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 13.2.0 h807b86a_5 conda-forge
libgettextpo 0.22.5 h59595ed_2 conda-forge
libgettextpo-devel 0.22.5 h59595ed_2 conda-forge
libgomp 13.2.0 h807b86a_5 conda-forge
libidn2 2.3.7 hd590300_0 conda-forge
libnghttp2 1.58.0 h47da74e_1 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libsqlite 3.45.2 h2797004_0 conda-forge
libssh2 1.11.0 h0841786_0 conda-forge
libstdcxx-ng 13.2.0 h7e041cc_5 conda-forge
libunistring 0.9.10 h7f98852_0 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
lxml 5.2.1 pypi_0 pypi
markdown-it-py 3.0.0 pypi_0 pypi
mdurl 0.1.2 pypi_0 pypi
menetools 3.4.0 pypi_0 pypi
metage2metabo 1.6.1 pypi_0 pypi
miscoto 3.2.0 pypi_0 pypi
mpmath 1.3.0 pypi_0 pypi
mpwt 0.8.6 pypi_0 pypi
ncbi-vdb 3.1.0 h4ac6f70_1 bioconda
ncurses 6.4.20240210 h59595ed_0 conda-forge
networkx 3.2.1 pypi_0 pypi
numpy 1.26.4 pypi_0 pypi
openssl 3.2.1 hd590300_1 conda-forge
optlang 1.8.1 pypi_0 pypi
packaging 24.0 pypi_0 pypi
padmet 5.0.1 pypi_0 pypi
pandas 2.2.2 pypi_0 pypi
pcre 8.45 h9c3ff4c_0 conda-forge
perl 5.32.1 7_hd590300_perl5 conda-forge
perl-archive-tar 2.40 pl5321hdfd78af_0 bioconda
perl-carp 1.38 pl5321hdfd78af_4 bioconda
perl-common-sense 3.75 pl5321hdfd78af_0 bioconda
perl-compress-raw-bzip2 2.201 pl5321h87f3376_1 bioconda
perl-compress-raw-zlib 2.105 pl5321h87f3376_0 bioconda
perl-encode 3.19 pl5321hec16e2b_1 bioconda
perl-exporter 5.72 pl5321hdfd78af_2 bioconda
perl-exporter-tiny 1.002002 pl5321hdfd78af_0 bioconda
perl-extutils-makemaker 7.70 pl5321hd8ed1ab_0 conda-forge
perl-io-compress 2.201 pl5321hdbdd923_2 bioconda
perl-io-zlib 1.14 pl5321hdfd78af_0 bioconda
perl-json 4.10 pl5321hdfd78af_0 bioconda
perl-json-xs 2.34 pl5321h4ac6f70_6 bioconda
perl-list-moreutils 0.430 pl5321hdfd78af_0 bioconda
perl-list-moreutils-xs 0.430 pl5321h031d066_2 bioconda
perl-parent 0.236 pl5321hdfd78af_2 bioconda
perl-pathtools 3.75 pl5321hec16e2b_3 bioconda
perl-scalar-list-utils 1.62 pl5321hec16e2b_1 bioconda
perl-types-serialiser 1.01 pl5321hdfd78af_0 bioconda
phasme 0.0.16 pypi_0 pypi
pip 24.0 pyhd8ed1ab_0 conda-forge
pluggy 1.4.0 pypi_0 pypi
powergrasp 0.8.18 pypi_0 pypi
pycparser 2.22 pypi_0 pypi
pydantic 2.7.0 pypi_0 pypi
pydantic-core 2.18.1 pypi_0 pypi
pydot 2.0.0 pypi_0 pypi
pyfaidx 0.8.1.1 pypi_0 pypi
pygments 2.17.2 pypi_0 pypi
pyparsing 3.1.2 pypi_0 pypi
pypeg2 2.15.2 pypi_0 pypi
pytest 8.1.1 pypi_0 pypi
python 3.9.19 h0755675_0_cpython conda-forge
python-dateutil 2.9.0.post0 pypi_0 pypi
python-graphviz 0.20.3 pypi_0 pypi
python-libsbml 5.20.2 pypi_0 pypi
pytz 2024.1 pypi_0 pypi
readline 8.2 h8228510_1 conda-forge
rich 13.7.1 pypi_0 pypi
ruamel-yaml 0.18.6 pypi_0 pypi
ruamel-yaml-clib 0.2.8 pypi_0 pypi
setuptools 69.2.0 pyhd8ed1ab_0 conda-forge
simplejson 3.19.2 pypi_0 pypi
six 1.16.0 pypi_0 pypi
sniffio 1.3.1 pypi_0 pypi
swiglpk 5.0.10 pypi_0 pypi
sympy 1.12 pypi_0 pypi
tk 8.6.13 noxft_h4845f30_101 conda-forge
tomli 2.0.1 pypi_0 pypi
typing-extensions 4.11.0 pypi_0 pypi
tzdata 2024.1 pypi_0 pypi
wget 1.21.4 hda4d442_0 conda-forge
wheel 0.43.0 pyhd8ed1ab_1 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
zipp 3.18.1 pypi_0 pypi
zlib 1.2.13 hd590300_5 conda-forge
zstd 1.5.5 hfc55251_0 conda-forge

[ArnaudBelcour]

Thank you for the versions of your environment. I think that the error comes from the interaction between an old version of Pathway Tools (22.5 or 23.0), that produces the warning No protein-coding genes with sequence data found and the last version of mpwt.

A first test could be to see if your version of Pathway Tools has the latest patches for its version number by running pathway-tools -id. When running pathway-tools command, it will try to update itself with the latest patches of its version with potential log looking like Downloading XX updated patches. If this is the case, try again to run mpwt. If not, try one of the following other processes:

Do you have the possibility to update to a more recent version of Pathway Tools (such as 27.5 or 28.0) or are you stuck with these versions?
I think updating Pathway Tools version could be the more robust fix for this issue.

If you cannot, another way possible could be to use an older version of mpwt that could tolerate these warnings. To this end, I think that the version 0.5.3 could handle these warnings (as it was one of the corresponding version of mpwt for Pathway Tools 23.0). But I think there will be issues with metage2metabo and potential errors present in old version of mpwt.