CMD ERROR: pasa_asmbls_to_training_set.dbi; cdna_alignment_orf_to_genome_orf.pl: not found

[eggrandio]

Hello,

I am trying to use the conda version of funannotate with a fungal genome. I have run all the tests successfully, but when I am using funannotate train on my data, everything goes well until PASA models are used to train TransDecoder. In the main output I get this error:

[12/03/25 19:13:16]: Getting PASA models for training with TransDecoder
[12/03/25 19:13:16]: /home/eggrandio/miniconda3/envs/funannotate/opt/pasa-2.5.3/scripts/pasa_asmbls_to_training_set.dbi --pasa_transcripts_fasta Penicillium_paxilli_pasa.assemblies.fasta --pasa_transcripts_gff3 Penicillium_paxilli_pasa.pasa_assemblies.gff3
[12/03/25 19:25:18]: CMD ERROR: /home/eggrandio/miniconda3/envs/funannotate/opt/pasa-2.5.3/scripts/pasa_asmbls_to_training_set.dbi --pasa_transcripts_fasta Penicillium_paxilli_pasa.assemblies.fasta --pasa_transcripts_gff3 Penicillium_paxilli_pasa.pasa_assemblies.gff3

When I look into the pasa-transdecoder.log it states that the cdna_alignment_orf_to_genome_orf.pl script cannot be found:

* [Wed Dec  3 19:24:54 2025] Running CMD: /home/eggrandio/miniconda3/envs/funannotate/opt/transdecoder/util/gff3_file_to_proteins.pl --gff3 /mnt/e/seq_data/2025_04_21_Ppax_genome/funannotate/train/training/pasa/Penicillium_paxilli_pasa.assemblies.fasta.transdecoder.gff3 --fasta Penicillium_paxilli_pasa.assemblies.fasta --seqType CDS  --genetic_code Universal > /mnt/e/seq_data/2025_04_21_Ppax_genome/funannotate/train/training/pasa/Penicillium_paxilli_pasa.assemblies.fasta.transdecoder.cds
Making cds file: /mnt/e/seq_data/2025_04_21_Ppax_genome/funannotate/train/training/pasa/Penicillium_paxilli_pasa.assemblies.fasta.transdecoder.cds
transdecoder is finished.  See output files /mnt/e/seq_data/2025_04_21_Ppax_genome/funannotate/train/training/pasa/Penicillium_paxilli_pasa.assemblies.fasta.transdecoder.*


CMD: cdna_alignment_orf_to_genome_orf.pl Penicillium_paxilli_pasa.assemblies.fasta.transdecoder.gff3 Penicillium_paxilli_pasa.pasa_assemblies.gff3 Penicillium_paxilli_pasa.assemblies.fasta > Penicillium_paxilli_pasa.assemblies.fasta.transdecoder.genome.gff3
sh: 1: cdna_alignment_orf_to_genome_orf.pl: not found
Error, cmd: cdna_alignment_orf_to_genome_orf.pl Penicillium_paxilli_pasa.assemblies.fasta.transdecoder.gff3 Penicillium_paxilli_pasa.pasa_assemblies.gff3 Penicillium_paxilli_pasa.assemblies.fasta > Penicillium_paxilli_pasa.assemblies.fasta.transdecoder.genome.gff3 died with ret 32512 at /home/eggrandio/miniconda3/envs/funannotate/opt/pasa-2.5.3/scripts/pasa_asmbls_to_training_set.dbi line 150.

However, when I look in the conda environment transdecoder folder, it is there:

~/miniconda3/envs/funannotate/opt/transdecoder/util$ ll cdna_alignment_orf_to_genome_orf.pl
-rwxr-xr-x 2 eggrandio eggrandio 12901 Jul 17 00:16 cdna_alignment_orf_to_genome_orf.pl*

Here arethe full funannotate-train.log and pasa-transdecoder.log for reference.

EDIT: I was able to fix it by manually setting the TransDecoder PATH:

echo 'export PATH="$CONDA_PREFIX/opt/transdecoder/util:$PATH"' >> /home/eggrandio/miniconda3/envs/funannotate/etc/conda/activate.d/funannotate.sh