Question: Error with gff file while building snpeff database
0
gravatar for kristina.mahan
11 days ago by
kristina.mahan110 wrote:

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?

java error snpeff gff • 116 views
ADD COMMENTlink modified 11 days ago by Fatima850 • written 11 days ago by kristina.mahan110
0
gravatar for Fatima
11 days ago by
Fatima850
United states
Fatima850 wrote:

/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
ADD COMMENTlink written 11 days ago by Fatima850

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.

ADD REPLYlink written 11 days ago by kristina.mahan110

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.

ADD REPLYlink written 11 days ago by Fatima850

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 . . .

ADD REPLYlink written 10 days ago by kristina.mahan110

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

ADD REPLYlink written 10 days ago by Fatima850

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.

ADD REPLYlink written 10 days ago by kristina.mahan110
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