cdsParts=true, but the ID (gene-si: )seems to be no CDS part about jstacs HOT 1 CLOSED

Hi Rich,

Thanks for the report.

I have downloaded the genome and the annotation from https://www.ncbi.nlm.nih.gov/genome/?term=txid7955[orgn] and ran the Extractor:

java -jar GeMoMa-1.9.jar CLI Extractor g=GCF_000002035.6_GRCz11_genomic.fna.gz a=GCF_000002035.6_GRCz11_genomic.gff.gz

which worked fine. So, you probably ran the complete pipeline and got the error from annother module. I had a closer look at the error message and wondered about the gene ID which is given as gene-si: (with a blank as last character an not further characters). Hence, I checked the annotation and found the several IDs have the pattern gene-si: .*. This might be a problem. The Extractor create FASTA file for the CDS-parts with the ID as prefix and the module GeMoMa cuts the part after the space while reading, as whitespace is often used as delimiter in FASTA. Hence, it will throw an error.

This error has been reported here: #39

For the moment, you can replace the whitespaces in your annotation mannually and run GeMoMa as before.
I have already implemented a solution with an additional parameter that will be released with the next version.

I hope that helps.

best regards, Jens

from jstacs.