Gemoma error with gff file

Question

[gubrins]

Hi all,

I am trying to annotate a new reference genome using the homology-based software GeMoMa. I already annotated a previous one and I want to use it as input for this second reference genome. However, it is displaying me this error regarding my first reference genome when running GeMoMa:

Extractor for species 7 (species7) throws an Exception
java.lang.NullPointerException
    at projects.gemoma.Extractor.read(Extractor.java:478)
    at projects.gemoma.Extractor.run(Extractor.java:107)
    at projects.gemoma.GeMoMaPipeline$JExtractorAndSplit.doJob(GeMoMaPipeline.java:1740)
    at projects.gemoma.GeMoMaPipeline$FlaggedRunnable.run(GeMoMaPipeline.java:1375)
    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:750)

java.lang.InterruptedException
    at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2072)
    at java.util.concurrent.ThreadPoolExecutor.awaitTermination(ThreadPoolExecutor.java:1475)
    at projects.gemoma.GeMoMaPipeline$1.run(GeMoMaPipeline.java:609)
    at projects.gemoma.GeMoMaPipeline$FlaggedRunnable.run(GeMoMaPipeline.java:1409)
    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:750)
No gene model was extracted from the references.

Statistics:
Job WAITING RUNNING INTERRUPTED FAILED  SUCCEEDED
---------------------------------------------------------
MmseqsCreateDB  0   1   0   0   0
EREAndFill  0   1   0   0   0
ExtractorAndSplit   0   7   0   1   0

Do you know what is going on? I am afraid the gff is in a bad format, but I do not understand the error. Thanks in advance!

[gubrins]

As a follow up, my first annotation was mannually mofidied in Geneious and then export it from there, could it be that Geneious is exporting it wrongly? Here I attach the first lines of the file, just in case:

##gff-version 3
##source-version geneious 2023.2.1
##sequence-region   CHR1    1   361990100
CHR1    GAF gene    45046   74882   .   +   .   Name=ADAMTSL5;ID=gene_13477
CHR1    GeMoMa  CDS 45046   45113   .   +   0   ID=agat-cds-30347;Parent=crotalus_tigris_rna-XM_039324357.1_R0
CHR1    AGAT    exon    45046   45113   .   +   .   ID=agat-exon-151193;Parent=crotalus_tigris_rna-XM_039324357.1_R0
CHR1    GeMoMa  mRNA    45046   74882   2564.0  +   .   Name=ADAMTSL5;ID=crotalus_tigris_rna-XM_039324357.1_R0;Dbxref=FunFam:G3DSA:2.60.120.830:FF:000001%2CGene3D:G3DSA:2.60.120.830%2CGene3D:G3DSA:2.20.100.10%2CGene3D:G3DSA:2.40.50.120%2CInterPro:IPR001134%2CInterPro:IPR018933%2CInterPro:IPR010294%2CInterPro:IPR008993%2CInterPro:IPR036383%2CInterPro:IPR000884%2CInterPro:IPR013273%2CInterPro:IPR045371%2CPANTHER:PTHR13723%2CPRINTS:PR01857%2CPfam:PF01759%2CPfam:PF05986%2CPfam:PF00090%2CPfam:PF19236%2CProSiteProfiles:PS50189%2CProSiteProfiles:PS50092%2CSMART:SM00209%2CSUPERFAMILY:SSF50242%2CSUPERFAMILY:SSF82895;Parent=gene_13477
CHR1    GeMoMa  CDS 46339   46399   .   +   1   ID=agat-cds-30348;Parent=crotalus_tigris_rna-XM_039324357.1_R0
CHR1    AGAT    exon    46339   46399   .   +   .   ID=agat-exon-151194;Parent=crotalus_tigris_rna-XM_039324357.1_R0
CHR1    GeMoMa  CDS 54755   54909   .   +   0   ID=agat-cds-30349;Parent=crotalus_tigris_rna-XM_039324357.1_R0

[Juke34]

It sounds geneiois made a mess (did it sort as tabix?). Maybe Gemoma needs transcripts features right after gene feature or some other sorting? You can try another pass of AGAT to re-sort this output before feeding GeMoMa.

[gubrins]

it seems that the annotation is lacking both parent and locus taggs. I executed agat_convert_sp_gxf2gxf.pl from AGAT and it solved it, but ideally I would like to avoid that step, as the new parent taggs have different names than the IDs I mannually wrote.