Entering edit mode
10 months ago
gubrins
▴
350
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!
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:
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.
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.