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Error while running SNPEff

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

snp
• 2,363 views • link
updated by Joe Joe • written by aditigrawal • aditigrawal

aditigrawal, can you try this and please respond? - it is the courteous thing to do after somebody tries to help you.

• 0 views • link
written by Kevin Blighe Kevin Blighe

Hi Kevin, I am so sorry to disappoint you. I just saw your reply and now I am replying you. So, what are you suggesting me to try?

• 0 views • link
written by aditigrawal • 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

• 0 views • link
written by aditigrawal • aditigrawal

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