ruy-jauregui commented 2 years ago

I have installed the Conda package version 1.8.13 check throws these errors: ruy@inv:/dataset/funannotate$ funannotate check

Checking dependencies for 1.8.13

To print all dependencies and versions: funannotate check --show-versions

You are running Python v 3.8.13. Now checking python packages... All 11 python packages installed

You are running Perl v b'5.032001'. Now checking perl modules... All 27 Perl modules installed

Checking Environmental Variables... ERROR: GENEMARK_PATH not set. export GENEMARK_PATH=/path/to/dir

Checking external dependencies... pigz 2.3.4 ERROR: emapper.py not installed ERROR: gmes_petap.pl not installed ERROR: pigz not installed

And yet, pigz is there. I don't know where to look for the missing Python and Perl scripts. ruy@inv:/dataset/funannotate$ which pigz /usr/bin/pigz

funannotate test -t predict hangs here:

######################################################### Running `funannotate predict` unit testing CMD: funannotate predict -i test.softmasked.fa --protein_evidence protein.evidence.fasta -o annotate --augustus_species saccharomyces --cpus 2 --species Awesome testicus #########################################################

[Oct 26 02:10 PM]: OS: CentOS Linux 7, 24 cores, ~ 396 GB RAM. Python: 3.8.13 [Oct 26 02:10 PM]: Running funannotate v1.8.13 [Oct 26 02:10 PM]: GeneMark not found and $GENEMARK_PATH environmental variable missing. Will skip GeneMark ab-initio prediction.

nothing happens after days waiting, assigning more threads doesn't change this.

Any help is greatly appreciated

hyphaltip commented 2 years ago

Yeah this is reported earlier. Working on test fix. What version of Augustus installed ?

ruy-jauregui commented 2 years ago

The bundled Augustus version on the Conda package is 3.5.0

nextgenusfs commented 2 years ago

Please upgrade to latest in master which I think the problem is fixed, its just not in a tagged release yet.

ruy-jauregui commented 2 years ago

Thanks. The latest master throws an error on the matplotlib version: /dataset/bioinformatics_dev/itmp/jaureguir/funannotate-011122/funannotate-master$ python3.10 setup.py install --prefix /dataset/bioinformatics_dev/itmp/jaureguir/funannotate-011122 ... Installed /bifo/itmp/bioinformatics_dev/jaureguir/funannotate-011122/lib/python3.10/site-packages/contourpy-1.0.6-py3.10-linux-x86_64.egg error: matplotlib 3.6.1 is installed but matplotlib!=3.6.1,>=3.1 is required by {'seaborn'}

nextgenusfs commented 2 years ago

python -m pip install .... --upgrade --force --no-deps

ruy-jauregui commented 2 years ago

Sorry, unless I'm not catching up, It doesn't help. jaureguir@invbfopp10:/dataset/bioinformatics_dev/itmp/jaureguir/funannotate-011122/funannotate-master$ python3.10 -m pip install matplotlib --upgrade --force --no-deps Collecting matplotlib Using cached matplotlib-3.6.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.8 MB) Installing collected packages: matplotlib Attempting uninstall: matplotlib Found existing installation: matplotlib 3.6.1 Uninstalling matplotlib-3.6.1: Successfully uninstalled matplotlib-3.6.1 Successfully installed matplotlib-3.6.1 this is the same version that throws the error. The error stays the same: error: matplotlib 3.6.1 is installed but matplotlib!=3.6.1,>=3.1 is required by {'seaborn'}

ruy-jauregui commented 2 years ago

Further confusion: This seems to run OK: python3.10 -m pip install matplotlib==3.6.0 --force --no-deps

and yet the error stays the same...

I even tried installing matplotlib 3.6.0 as a conda environment, but the error stays.

nextgenusfs / funannotate

check errors, test predict hangs #823

and yet the error stays the same...