Which is the ultimate Augustus version that works with the latest funannotate?

[BrigidaGallone]

Hello, I am struggling with Funannotate installation for a while and was hoping you could help me figuring it out how to make it work. For the installation I followed exactly the installation guide and used conda.

Are you using the latest release? Yes, version v1.8.13 installed via conda a week ago.

Describe the bug During the test run: funannotate test -t predict --cpus ${SLURM_CPUS_PER_TASK}

The step predict fails with error: [Feb 10 03:26 PM]: augustus: ERROR Could not locate command line parameters file: annotate/predict_misc/ab_initio_parameters/augustus/parameters/aug_cmdln_parameters.json.

The error is the same as issue https://github.com/nextgenusfs/funannotate/issues/776 but after a lot of trials and errors it is unclear to me which Augustus version and file (locally/in conda/etc.) to use to run the latest version of funannotate.

What command did you issue? funannotate test -t predict --cpus ${SLURM_CPUS_PER_TASK}

Logfiles

OS/Install Information Checking dependencies for 1.8.13

You are running Python v 3.8.15. Now checking python packages... biopython: 1.80 goatools: 1.2.3 matplotlib: 3.4.3 natsort: 8.2.0 numpy: 1.24.1 pandas: 1.5.3 psutil: 5.9.4 requests: 2.28.2 scikit-learn: 1.2.1 scipy: 1.10.0 seaborn: 0.12.2 All 11 python packages installed

You are running Perl v b'5.032001'. Now checking perl modules... Carp: 1.38 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 threads: 2.25 threads::shared: 1.61 ERROR: local::lib not installed, install with cpanm local::lib

Checking Environmental Variables... $FUNANNOTATE_DB=/data1/bgallone/funannotate/funannotate_db $PASAHOME=/data1/bgallone/conda/envs/funannotate/opt/pasa-2.5.2 $TRINITY_HOME=/data1/bgallone/conda/envs/funannotate/opt/trinity-2.8.5 $EVM_HOME=/data1/bgallone/conda/envs/funannotate/opt/evidencemodeler-1.1.1 $AUGUSTUS_CONFIG_PATH=/data1/bgallone/conda/envs/funannotate/config/ ERROR: GENEMARK_PATH not set. export GENEMARK_PATH=/path/to/dir

Checking external dependencies... PASA: 2.5.2 CodingQuarry: 2.0 Trinity: 2.8.5 augustus: 3.5.0 bamtools: bamtools 2.5.1 bedtools: bedtools v2.30.0 blat: BLAT v35 diamond: 2.0.15 ete3: 3.1.2 exonerate: exonerate 2.4.0 fasta: no way to determine glimmerhmm: 3.0.4 gmap: 2021-08-25 hisat2: 2.2.1 hmmscan: HMMER 3.3.2 (Nov 2020) hmmsearch: HMMER 3.3.2 (Nov 2020) java: 17.0.3-internal kallisto: 0.46.1 mafft: v7.515 (2023/Jan/15) makeblastdb: makeblastdb 2.2.31+ minimap2: 2.24-r1122 proteinortho: 6.1.7 pslCDnaFilter: no way to determine salmon: salmon 0.14.1 samtools: samtools 1.16.1 snap: 2006-07-28 stringtie: 2.2.1 tRNAscan-SE: 2.0.11 (Oct 2022) tantan: tantan 40 tbl2asn: no way to determine, likely 25.X tblastn: tblastn 2.2.31+ trimal: trimAl v1.4.rev15 build[2013-12-17] trimmomatic: 0.39 ERROR: emapper.py not installed ERROR: gmes_petap.pl not installed ERROR: pigz not installed ERROR: signalp not installed

[nextgenusfs]

With funannotate v1.8.13 you have to use Augustus < 3.4.

[BrigidaGallone]

Thank you very much for your help! I will try that and close the issue for the moment.