Error with gff file while building snpeff database

I built a snpEff database for my nuclear genome. It worked. I am now trying to build own for the chloroplast and mitochondria genomes. I've edited the config file and I have fasta files in the genome folder and their corresponding .gff files in their respective folders. I'm getting this error after I run the build command:

Reading GFF3 data file  : '/home/kmmahan/snpEff/./data/scenedesmus_obliquus_doe0152z_mitochondria/genes.gff'
java.lang.StackOverflowError

I checked the fasta file and the gff file and the genome names match. It's not a memory error because I was able to build the nuclear genome database. I get the error for both the chloroplast and mitochondria database. I've searched for answers on biostars but I am stuck. Something seems to be wrong when it tries to read the gff file. What changes can I make?

gff java snpeff

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updated 2.9 years ago by Ram

• written 5.7 years ago by kristina.mahan

1 answer

/snpEff/./data/

I'm not sure, but this "." in the path seems weird to me. Are you sure the path is correct?

ls /home/kmmahan/snpEff/./data/scenedesmus_obliquus_doe0152z_mitochondria/genes.gff

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written 5.7 years ago by Fatima

It's the same path I used for the nuclear genome (except folder was scenedesmus_obliquus_doe0152z_nuclear/genes.gff). And same way that it was done here: A: Building Snpeff Database

I cd's using the path you listed (/home/kmmahan/snpEff/./data/scenedesmus_obliquus_doe0152z_mitochondria) and was taken to that directory. I think the path is correct.

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written 5.7 years ago by kristina.mahan

Oh, okay. What did you use to read the gff file? That program probably makes a lot of recursive calls, that fills up the stack.

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written 5.7 years ago by Fatima

What do you mean read? I just entered the build command to build the database11. java -jar snpEff.jar build -gff3 -v scenedesmus_obliquus_doe0152z_mitochondria

Oh maybe its the -gff3? Except I used the same thing to build the database for the nuclear genome . . .

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written 5.7 years ago by kristina.mahan

Yes, -gff3 probably calls a different set of functions.

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written 5.7 years ago by Fatima

If I am using a gff file- I have to put -gff3 in the build command. Also - I used -gffs to build the database for the nuclear genome and it worked. Something seems to be wrong with the gff files themselves but just haven't figured it out.

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written 5.7 years ago by kristina.mahan