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nextgenusfs / funannotate

Eukaryotic Genome Annotation Pipeline
http://funannotate.readthedocs.io
BSD 2-Clause "Simplified" License
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TransDecoder.Predict error died with ret 512 whilst running pasa_asmbls_to_training_set.dbi #560

Closed Rob-murphys closed 3 years ago

Rob-murphys commented 3 years ago

Input funannotate train -i $input -o $outdir --left $rnaLeft --right $rnaRight --stranded $stranded

Error I am getting this error: Error, cmd: TransDecoder.Predict -t IC0001_sorted_masked.assemblies.fasta died with ret 512 at /services/tools/funannotate/1.8.3/opt/pasa/scripts/pasa_asmbls_to_training_set.dbi line 148.

Seems to be as a result of: No such file or directory at /services/tools/funannotate/1.8.3/opt/transdecoder/PerlLib/Pipeliner.pm line 185.

Whole error report is here: funannotate_train-call.sh.e30742184.zip

Any help would be appreciated.

nextgenusfs commented 3 years ago

Here: https://github.com/PASApipeline/PASApipeline/issues/116 which links to several other issues -- the result seems to be there are not enough gene models to make the calculation.

[03:57 PM]: PASA assigned 99 transcripts to 96 loci (genes)

This is not from the test data, correct? If it is the test data then something upstream is wrong.

Rob-murphys commented 3 years ago

This is not from the test data. The transcripts being used are whole transcriptomes so there should be no lack of 5' UTRs. The genome itself is a symbiotic fungi which tend to have a lot of repeat regions if that could be causing it?

[03:57 PM]: PASA assigned 99 transcripts to 96 loci (genes)

Meaning it was only able to use the transcriptome to identify 99 genes? Hmm weird! Would you like the input data to see if something is going wrong?