Error while running SNPEff

Question

[aditigrawal]

Hi all, I am trying to build database from GTF file, I created from de novo assembled transcriptome using trinity.

I am using following command : java -jar snpEff.jar build -gtf22 -v PBW

and getting this error:

Picked up _JAVA_OPTIONS: -Xmx1g
00:00:00        SnpEff version SnpEff 4.3t (build 2017-11-24 10:18), by Pablo Cingolani
00:00:00        Command: 'build'
00:00:00        Building database for 'PBW'
00:00:00        Reading configuration file 'snpEff.config'. Genome: 'PBW'
00:00:00        Reading config file: /home/aditi/snpEff/snpEff.config
00:00:00        done
Reading GTF22 data file  : '/home/aditi/snpEff/./data/PBW/genes.gtf'
java.lang.StackOverflowError
        at java.lang.Character.toLowerCase(Character.java:6338)
        at java.lang.Character.toLowerCase(Character.java:6309)
        at java.lang.String.toLowerCase(String.java:2581)
        at java.lang.String.toLowerCase(String.java:2670)
        at org.snpeff.interval.GffMarker.hasAttr(GffMarker.java:208)
        at org.snpeff.interval.GffMarker.getTranscriptId(GffMarker.java:189)
        at org.snpeff.interval.GffMarker.getGffParentId(GffMarker.java:149)
        at org.snpeff.interval.GffMarker.getTranscriptId(GffMarker.java:191)
        at org.snpeff.interval.GffMarker.getGffParentId(GffMarker.java:149)
        at org.snpeff.interval.GffMarker.getTranscriptId(GffMarker.java:191)
        at org.snpeff.interval.GffMarker.getGffParentId(GffMarker.java:149)
        at org.snpeff.interval.GffMarker.getTranscriptId(GffMarker.java:191)
        at org.snpeff.interval.GffMarker.getGffParentId(GffMarker.java:149)
        at org.snpeff.interval.GffMarker.getTranscriptId(GffMarker.java:191)
        at org.snpeff.interval.GffMarker.getGffParentId(GffMarker.java:149)
        at org.snpeff.interval.GffMarker.getTranscriptId(GffMarker.java:191)
        at org.snpeff.interval.GffMarker.getGffParentId(GffMarker.java:149)
        at org.snpeff.interval.GffMarker.getTranscriptId(GffMarker.java:191)
        at org.snpeff.interval.GffMarker.getGffParentId(GffMarker.java:149)
        at org.snpeff.interval.GffMarker.getTranscriptId(GffMarker.java:191)
        at org.snpeff.interval.GffMarker.getGffParentId(GffMarker.java:149)
        at org.snpeff.interval.GffMarker.getTranscriptId(GffMarker.java:191)
        at org.snpeff.interval.GffMarker.getGffParentId(GffMarker.java:149)
        at org.snpeff.interval.GffMarker.getTranscriptId(GffMarker.java:191)
        at org.snpeff.interval.GffMarker.getGffParentId(GffMarker.java:149)
        at org.snpeff.interval.GffMarker.getTranscriptId(GffMarker.java:191)
        at org.snpeff.interval.GffMarker.getGffParentId(GffMarker.java:149)
        at org.snpeff.interval.GffMarker.getTranscriptId(GffMarker.java:191)
        at org.snpeff.interval.GffMarker.getGffParentId(GffMarker.java:149)
        at org.snpeff.interval.GffMarker.getTranscriptId(GffMarker.java:191)
        at org.snpeff.interval.GffMarker.getGffParentId(GffMarker.java:149)
        at org.snpeff.interval.GffMarker.getTranscriptId(GffMarker.java:191)
        at org.snpeff.interval.GffMarker.getGffParentId(GffMarker.java:149)
        at org.snpeff.interval.GffMarker.getTranscriptId(GffMarker.java:191)
        at org.snpeff.interval.GffMarker.getGffParentId(GffMarker.java:149)
        at org.snpeff.interval.GffMarker.getTranscriptId(GffMarker.java:191)

can somebody please help me in this.

Thanks

[jean.elbers]

Maybe try increasing the stack size (see https://examples.javacodegeeks.com/java-basics/exceptions/java-lang-stackoverflowerror-how-to-solve-stackoverflowerror/)

 java -Xss1M -jar snpEff.jar build -gtf22 -v PBW

Or increase -Xss to something larger if -Xss1M doesn't work.

[aditigrawal]

Hi, Thank you for your reply. I did try increasing the stack size. It did not work. Apparently, the problem is with GTF file, I did try with other GFF file and it is running successfully.

I checked my GTF file, it looks ok to me, can you suggest something in the regards.

Thanks

[Kevin Blighe]

Great - thank you! :)