Augustus error: Unknown parameter: "softmasking".

[Arkadiy-Garber]

Did a fresh conda/mamba install yesterday and getting the following error (many iterations of the same error in the same run:

(funannotate) MAB@Axceleron-WKS:~/done/3323/raw/assembly1$ funannotate predict -i contigs.masked.sorted.clean.fasta -o predictions -s "Saccharomyces cerevisiae" --cpus 24
-------------------------------------------------------
[Jul 25 03:22 PM]: OS: Ubuntu 22.04, 80 cores, ~ 264 GB RAM. Python: 3.8.15
[Jul 25 03:22 PM]: Running funannotate v1.8.15
[Jul 25 03:22 PM]: GeneMark not found and $GENEMARK_PATH environmental variable missing. Will skip GeneMark ab-initio prediction.
[Jul 25 03:22 PM]: Skipping CodingQuarry as no --rna_bam passed
[Jul 25 03:22 PM]: Parsed training data, run ab-initio gene predictors as follows:
  Program      Training-Method
  augustus     busco          
  glimmerhmm   busco          
  snap         busco          
[Jul 25 03:23 PM]: Loading genome assembly and parsing soft-masked repetitive sequences
[Jul 25 03:23 PM]: Genome loaded: 6,231 scaffolds; 57,146,367 bp; 5.12% repeats masked
/data/MAB/miniconda3/envs/funannotate/lib/python3.8/site-packages/funannotate/aux_scripts/funannotate-p2g.py:14: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
  from pkg_resources import parse_version
[Jul 25 03:23 PM]: Mapping 556,939 proteins to genome using diamond and exonerate
[Jul 25 03:25 PM]: Found 615,614 preliminary alignments with diamond in 0:01:31 --> generated FASTA files for exonerate in 0:00:32
     Progress: 615614 complete, 0 failed, 0 remaining             
[Jul 25 04:11 PM]: Exonerate finished in 0:45:20: found 2,537 alignments
[Jul 25 04:11 PM]: Running BUSCO to find conserved gene models for training ab-initio predictors
[Jul 25 04:16 PM]: 1,283 valid BUSCO predictions found, validating protein sequences
[Jul 25 04:17 PM]: 1,283 BUSCO predictions validated
[Jul 25 04:17 PM]: Training Augustus using BUSCO gene models
[Jul 25 04:18 PM]: Augustus initial training results:
  Feature       Specificity   Sensitivity
  nucleotides   97.7%         96.9%      
  exons         85.2%         81.0%      
  genes         68.8%         58.7%      
[Jul 25 04:18 PM]: Running Augustus gene prediction using saccharomyces_cerevisiae parameters
[Jul 25 04:18 PM]: CMD ERROR: augustus --species=saccharomyces_cerevisiae --extrinsicCfgFile=/data/MAB/miniconda3/envs/funannotate/lib/python3.8/site-packages/funannotate/config/extrinsic.E.XNT.RM.cfg --hintsfile=predictions/predict_misc/hints.ALL.gff --AUGUSTUS_CONFIG_PATH=predictions/predict_misc/ab_initio_parameters/augustus --softmasking=1 --gff3=on --UTR=off --stopCodonExcludedFromCDS=False augustus_tmp_f4a6112c-f16b-4ffd-8471-69a462d669de/scaffold_6.fa
[Jul 25 04:18 PM]: 
augustus: ERROR
    Unknown parameter: "softmasking". Type "augustus" for help.

Thanks, Arkadiy

[Arkadiy-Garber]

Following this, the script gets hung up on:

[Jul 25 04:18 PM]: CMD ERROR: augustus --species=saccharomyces_cerevisiae --extrinsicCfgFile=/data/MAB/miniconda3/envs/funannotate/lib/python3.8/site-packages/funannotate/config/extrinsic.E.XNT.RM.cfg --hintsfile=predictions/predict_misc/hints.ALL.gff --AUGUSTUS_CONFIG_PATH=predictions/predict_misc/ab_initio_parameters/augustus --softmasking=1 --gff3=on --UTR=off --stopCodonExcludedFromCDS=False augustus_tmp_f4a6112c-f16b-4ffd-8471-69a462d669de/scaffold_6231.fa
[Jul 25 04:18 PM]: 
augustus: ERROR
    Unknown parameter: "softmasking". Type "augustus" for help.

     Progress: 0 complete, 0 failed, 6233 remaining    

[nextgenusfs]

What version and build of augustus?

[Arkadiy-Garber]

So it looks like my PATH was pointed towards some version 2.5 that I had previously install.

Removing that path and manually inserting the path to the conda build version 3.5 fixed this.

Thanks for your prompt response!