RuntimeException about jstacs HOT 4 CLOSED

Hi Qingying,

Thanks for your interest in GeMoMa and for reporting this issue. I have looked into the log file and saw that the run was almost finished. Hence, GeMoMa-Temp contains the two files you reported. However, since version 1.8, we run SyntenyChecker at the end of GeMoMaPipeline. This module needs the assignment file. You did not use an assignment file and ran into a bug. Thanks for repoting. I'll fix it.

You can easily avoid this bug if you used sc=false, which switches off the use of SyntenyChecker.
You can even finished you broken run if you additionally use restart=true.
So to finish you run, you can use the following command line:
java -jar /home/qymeng/biosoft/GeMoMa/GeMoMa-1.8.jar CLI GeMoMaPipeline threads=10 AnnotationFinalizer.r=NO p=false o=true t=GCF_000004255.2_v.1.0_genomic.fna.gz outdir=output/ s=pre-extracted c=/home/qymeng/Gbarbadense/Annotation/Protein/Athaliana_447_Araport11.protein.fa sc=false restart=true >test-2.log 2>&1 &

Finally, I just like to make a point. GeMoMa was initially build to exploit the conservation of intron
Hence, it will provide better results if you use the reference annotation (e.g. a gff file) and the reference genome (e.g. a fasta file). You have used proteins (via the selection s=pre-extracted c=...protein.fa) which do not provide any information about intron position and hence cannot utilize valuable intron position conservation.
Arabidopsis thalina annotation and genome can be downloaded, for instance, from NCBI, Phytozome, ... and used directly as reference.

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I fixed it: 7712e13
Will be included in the next release.

from jstacs.

Thanks for your quick answer and suggests, I have got the result with no errors.
Best wishes;

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Great news.
Best regards, Jens

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