Error message running GeMoMa

Question

[valopes]

I am trying to run GeMoMa for gene annotation using RNA-seq evidence.

java -jar -Xms25G -Xmx50G GeMoMa-1.6.1.jar CLI GeMoMaPipeline t=target.fasta s=own a=ref-annotation.gff  g=ref.fa outdir=test r=MAPPED ERE.s=FR_UNSTRANDED ERE.m=target-accepted_hits.bam  ERE.v=SILENT ERE.c=true tblastn=true Extractor.p=true Extractor.r=true Extractor.s=true Extractor.f=true AnnotationFinalizer.u=YES AnnotationFinalizer.r=NO p=true pc=true pgr=true

However, I am getting this error message:

> starting extractor for species 0

> java.lang.StringIndexOutOfBoundsException: String index out of range:
> -1    at java.lang.String.charAt(String.java:658)     at projects.gemoma.Extractor.transcript(Extractor.java:835)     at
> projects.gemoma.Extractor.extract(Extractor.java:667)     at
> projects.gemoma.Extractor.run(Extractor.java:142)     at
> projects.gemoma.GeMoMaPipeline$JExtractorAndSplit.doJob(GeMoMaPipeline.java:1166)
>   at
> projects.gemoma.GeMoMaPipeline$FlaggedRunnable.run(GeMoMaPipeline.java:937)
>   at
> java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
>   at java.util.concurrent.FutureTask.run(FutureTask.java:266)     at
> java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
>   at java.util.concurrent.FutureTask.run(FutureTask.java:266)     at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
>   at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
>   at java.lang.Thread.run(Thread.java:748)
> 
> 
> Statistics: Job   WAITING RUNNING INTERRUPTED FAILED  SUCCEEDED
> --------------------------------------------------------- MakeBlastDB 0   0   0   0   1 EREAndFill    1   0   0   0   0
> 
> ExtractorAndSplit 0   0   0   1   0
> 
> 2 jobs did not finish as expected. Please check the output carefully.
> Did not delete temporary files allowing to debug.
> 
> Elapsed time: 15 seconds  (0h 0m 15s) Exception in thread "main"
> java.lang.RuntimeException: Did not finish as intended. String index
> out of range: -1  at java.lang.String.charAt(String.java:658)     at
> projects.gemoma.Extractor.transcript(Extractor.java:835)  at
> projects.gemoma.Extractor.extract(Extractor.java:667)     at
> projects.gemoma.Extractor.run(Extractor.java:142)     at
> projects.gemoma.GeMoMaPipeline$JExtractorAndSplit.doJob(GeMoMaPipeline.java:1166)
>   at projects.gemoma.GeMoMaPipeline$FlaggedRunnable.run(GeMoMaPipeline.java:937)
>   at
> java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
>   at java.util.concurrent.FutureTask.run(FutureTask.java:266)     at
> java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
>   at java.util.concurrent.FutureTask.run(FutureTask.java:266)     at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
>   at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
>   at java.lang.Thread.run(Thread.java:748)

I think I've tried everything I know. Does anyone could please help me?

[GenoMax]

I am not sure what version of GeMoMa you are running but looking at the manual your command line is different than the one in the manual.

Have you run test.sh to check your install? I would suggest using the shell pipelines (run.sh and pipeline.sh) mentioned in the manual once test.sh works.

[valopes]

Hi! Thanks for your answer...

So I test every thing and it is working fine!

But even I am getting no Error message and generates all files, it returns me a empty gff3 file and empty protein.fasta file as well...

That is the messages I got:

Adding sequences from FASTA; added 7464 sequences in 14.2187 seconds. genome parts: 7464    [scaffold_6170, scaffold_6172, scaffold_6171, scaffold_6163, scaffold_6162, scaffold_6165, scaffold_6164, scaffold_6167, scaffold_6166, scaffold_6169, scaffold_6168, scaffold_6161, scaffold_6160, scaf... possible introns from RNA-seq (split reads>=1): 0
+: 0
-: 0 .: 0 Check RNA-seq data (introns): 0% of the sequences in the reference genome are covered.

starting phase 2
================ species 0: 3 splits starting tblastn split=0 for species 0 starting tblastn split=2 for species 0 starting tblastn split=1 for species 0 starting GeMoMa split=1 for species 0 starting GeMoMa split=0 for species 0 starting GeMoMa split=2 for species 0

starting phase 3
================ starting cat for species 0

starting phase 4
================ starting GAF

starting phase 5
================ starting AnnotationFinalizer

starting phase 6
================ starting extractor for final prediction

Statistics: Job WAITING RUNNING INTERRUPTED FAILED  SUCCEEDED
--------------------------------------------------------- MakeBlastDB   0   0   0   0   1 EREAndFill    0   0   0   0   1

ExtractorAndSplit   0   0   0   0   1 Tblastn   0   0   0   0   3 GeMoMa    0   0   0   0   3 Cat   0   0   0   0   1 GAF   0   0   0   0   1

AnnotationFinalizer 0   0   0   0   1 Extractor 0   0   0   0   1

No errors detected. Elapsed time: 71 seconds    (0h 1m 11s)

real    3m23.882s user  2m14.768s sys   0m7.339s

If you could please help me?

[valopes]

plus with or without RNA-seq data I still dont get anything

[GenoMax]

Sorry I have never used this program so can't directly assist but it appears that there may be something wrong in phase 1 itself: 0% of the sequences in the reference genome are covered.

[valopes]

Thanks anyway, genomax!

[ning.zhang19890114]

Hi ! I met the same error.. So,had you solved it already?

[valopes]

Hi! I figured that my gff file was completely out of the format. So after a fixed, it worked fine.

[mharrison]

Hi valopes, I'm getting the same error but as far as I can see my gff is ok. Can you remember what specifically was wrong with your gff? Thanks, Mark

[Dardo]

can you solve this problem? this is my problem too

[Melisa]

Im having the same problem but when I add external ab initio annotations:

java -jar -Xms120g -Xmx120g GeMoMa-1.9.jar CLI GeMoMaPipeline t=genome.fasta threads=10 outdir=resultUTRensgtf p=false o=true s=own i=montanus a=relatedspecie.gff g=relatedspecie.fna GAF.a="pAA>=0.8" AnnotationFinalizer.u=YES r=MAPPED ERE.sorted.bam  ID=braker e=braker.gff 

Statistics:
Job WAITING RUNNING INTERRUPTED FAILED  SUCCEEDED
---------------------------------------------------------
MmseqsCreateDB  0   0   0   0   1
EREAndFill  0   0   0   0   1
ExtractorAndSplit   0   0   0   0   1
Mmseqs  0   0   0   0   1
GeMoMa  0   0   0   0   10
Cat 0   0   0   0   1
AnnotationEvidence  0   0   0   0   1
GAF 0   0   0   0   1
AnnotationFinalizer 0   0   0   0   1

Did not delete temporary files allowing to debug.

Elapsed time: 39 seconds    (0h 0m 39s)
Exception in thread "main" java.lang.RuntimeException: Did not finish as intended. java.lang.NullPointerException: null
    at projects.gemoma.GeMoMaPipeline.run(GeMoMaPipeline.java:1038)
    at projects.gemoma.GeMoMaModule.run(GeMoMaModule.java:94)
    at de.jstacs.tools.ui.cli.CLI.run(CLI.java:426)
    at projects.gemoma.GeMoMa.main(GeMoMa.java:399)

I can see my gff is ok. Can you remember what specifically was wrong with your gff? Thanks, Melisa