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nextgenusfs / funannotate

Eukaryotic Genome Annotation Pipeline
http://funannotate.readthedocs.io
BSD 2-Clause "Simplified" License
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Error with gmap when checking dependencies #883

Open tjhinet opened 1 year ago

tjhinet commented 1 year ago

Hi,

I am having issues with gmap when I am checking Funannotate dependencies. I have created a conda environment for funannotate and installed funannotate with mamba. It looks like gmap (v2021.08.25) and pasa (v2.5.2) have been installed but the following error comes up when I perform "funannotate check --show-versions":

Checking dependencies for 1.8.13

You are running Python v 3.8.15. Now checking python packages... biopython: 1.81 goatools: 1.2.3 matplotlib: 3.4.3 natsort: 8.3.1 numpy: 1.24.2 pandas: 1.5.3 psutil: 5.9.4 requests: 2.28.2 scikit-learn: 1.2.2 scipy: 1.10.1 seaborn: 0.12.2 All 11 python packages installed

You are running Perl v b'5.032001'. Now checking perl modules... Carp: 1.50 Clone: 0.46 DBD::SQLite: 1.72 DBD::mysql: 4.046 DBI: 1.643 DB_File: 1.855 Data::Dumper: 2.183 File::Basename: 2.85 File::Which: 1.24 Getopt::Long: 2.54 Hash::Merge: 0.302 JSON: 4.10 LWP::UserAgent: 6.67 Logger::Simple: 2.0 POSIX: 1.94 Parallel::ForkManager: 2.02 Pod::Usage: 1.69 Scalar::Util::Numeric: 0.40 Storable: 3.15 Text::Soundex: 3.05 Thread::Queue: 3.14 Tie::File: 1.06 URI::Escape: 5.12 YAML: 1.30 local::lib: 2.000029 threads: 2.25 threads::shared: 1.61 All 27 Perl modules installed

Checking Environmental Variables... $FUNANNOTATE_DB=/home/u4485090/FUNANNOTATE_DB $PASAHOME=/home/u4485090/conda/envs/funannotate/opt/pasa-2.5.2 $TRINITY_HOME=/home/u4485090/conda/envs/funannotate/opt/trinity-2.8.5 $EVM_HOME=/home/u4485090/conda/envs/funannotate/opt/evidencemodeler-1.1.1 $AUGUSTUS_CONFIG_PATH=/home/u4485090/conda/envs/funannotate/config/ ERROR: GENEMARK_PATH not set. export GENEMARK_PATH=/path/to/dir

Checking external dependencies... ERROR: gmap found but error running gmap Traceback (most recent call last): File "/home/u4485090/conda/envs/funannotate/bin/ete3", line 6, in from ete3.tools.ete import main File "/home/u4485090/conda/envs/funannotate/lib/python3.8/site-packages/ete3/tools/ete.py", line 55, in from . import (ete_split, ete_expand, ete_annotate, ete_ncbiquery, ete_view, File "/home/u4485090/conda/envs/funannotate/lib/python3.8/site-packages/ete3/tools/ete_view.py", line 48, in from .. import (Tree, PhyloTree, TextFace, RectFace, faces, TreeStyle, CircleFace, AttrFace, ImportError: cannot import name 'TextFace' from 'ete3' (/home/u4485090/conda/envs/funannotate/lib/python3.8/site-packages/ete3/init.py) PASA: 2.5.2

Can I please get some help with this? I tried downgrading gmap and pasa to an older version but the installer refused to do it.

Thank you very much in advance!

Regards, Erick

hyphaltip commented 1 year ago

Did you install gmap by conda. I don't even think it works as well as exonerate so we don't make it a default.

tjhinet commented 1 year ago

I think in my case the gmap and pasa was installed as part of the Funannotate package through conda. I don't know if this error will be critical for what I want to do, but in my past genome annotation, I had performed it with Funannotate that has passed all of the dependencies.