GeMoMa error about jstacs HOT 8 OPEN

Hi sujianed,

thanks a lot for your interest in GeMoMa. I would be happy to help you.
Unfortunately, it seems that you have cut too much information. In addition, the error log and the standard out seems to be mixed. Could you please send more information, but split into standard out and error log?

best regards, Jens

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I can't seem to find the wrong information.When I use plants Poplustri Chocapa, Oriza Sativa, Japonica Glup, Arrábidop Staliana, Glesin Max, Vitis Vinnifila, are Oak's. note:All data is downloaded from ensembl
java -jar /share/work/biosoft/GeMoMa/GeMoMa-1.9/GeMoMa-1.9.jar CLI GeMoMaPipeline
threads=10 AnnotationFinalizer.r=NO p=false o=true tblastn=false
t=contig.hardmasked.fa outdir=gemoma
s=own i=ath a=Arabidopsis_thaliana.longest_isoform.gff3 g=$database/homo_protein/ath.fa.gz
s=own i=gma a=Glycine_max.longest_isoform.gff3 g=$database/homo_protein/gma.fa.gz
s=own i=vin a=Vitis_vinifera.longest_isoform.gff3 g=$database/homo_protein/vin.fa.gz
s=own i=ptr a=Populus_trichocarpa.longest_isoform.gff3 g=$database/homo_protein/ptr.fa.gz
s=own i=osa a=Oryza_sativa.longest_isoform.gff3 g=$database/homo_protein/osa.fa.gz

but,When I use animal Danio_rerio, Homo_sapiens, Leptobrachium_leishanense, Mus_musculus, Xenopus_tropicalis, it's not OK
java -jar /share/work/biosoft/GeMoMa/GeMoMa-1.9/GeMoMa-1.9.jar CLI GeMoMaPipeline
threads=200 AnnotationFinalizer.r=NO p=false o=true tblastn=false
t=contig.hardmasked.fa outdir=gemoma
s=own i=dr a=Danio_rerio.longest_isoform.gff3 g=dr.fa.gz
s=own i=hs a=Homo_sapiens.longest_isoform.gff3 g=hs.fa.gz
s=own i=ll a=Leptobrachium_leishanense.longest_isoform.gff3 g=ll.fa.gz
s=own i=mm a=Mus_musculus.longest_isoform.gff3 g=mm.fa.gz
s=own i=xt a=Xenopus_tropicalis.longest_isoform.gff3 g=xt.fa.gz

Oddly enough, when I use "java -jar /share/work/biosoft/GeMoMa/GeMoMa-1.9/GeMoMa-1.9.jar CLI GeMoMaPipeline
threads=200 AnnotationFinalizer.r=NO p=false o=true tblastn=false
t=contig.hardmasked.fa outdir=gemoma
s=own i=ll a=Leptobrachium_leishanense.longest_isoform.gff3 g=ll.fa.gz" it's OK

"java -jar /share/work/biosoft/GeMoMa/GeMoMa-1.9/GeMoMa-1.9.jar CLI GeMoMaPipeline
threads=200 AnnotationFinalizer.r=NO p=false o=true tblastn=false
t=contig.hardmasked.fa outdir=gemoma
s=own i=xt a=Xenopus_tropicalis.longest.longest_isoform.gff3 g=xt.fa.gz" it's OK

from jstacs.

Hi sujianed,

I'm sorry that you still have problems and it is hard for me to follow.

However, I realized

1. That you could run GeMoMa in principle. Hence, it should be no problem with installing GeMoMa, which is great.
2. That you could run GeMoMa on a part of the complete input. You wrote that it finished successfully with input Leptobrachium_leishanense.longest_isoform.gff3 and also with input Xenopus_tropicalis.longest.longest_isoform.gff3.
3. That you reported a problem with input "ll" and "mm" (cf. first post, interestingly the command line (ll, xt) and the output (ll, mm) are not matching). Hence, I would assume there is a problem with input "mm".

I would recommend to run GeMoMa independently for each input to see whether there is a problem for one input.

If you would send more information from the log, we could probably track the error more easily.

best regards, Jens

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Uploading 08.GeMoMa.sh.o.txt…

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##################################

mkdir 08.GeMoMa
cd 08.GeMoMa

#同源物种蛋白，GeMoMa比对

ln -s /work/annotion_edta/edta_anno/09.RepeatFinal/contig.hardmasked.fa contig.hardmasked.fa

#Danio rerio斑马鱼
#Homo sapiens智人
#Lithobates catesbeianus美洲牛蛙 NCBI上没有，只有Aquarana catesbeiana
#Mus musculus小家鼠
#Nanorana parkeri高山倭蛙
#Xenopus laevis非洲爪蟾
#Xenopus tropicalis热带爪蟾
ln -s /work/data/homo_protein/ensemble/v102/Danio_rerio.GRCz11.102.chr.gff3.gz dr.gff3.gz
ln -s /work/data/homo_protein/ensemble/v102/Danio_rerio.GRCz11.dna.toplevel.fa.gz dr.fa.gz
ln -s /work/data/homo_protein/ensemble/v102/Homo_sapiens.GRCh38.102.chr.gff3.gz hs.gff3.gz
ln -s /work/data/homo_protein/ensemble/v102/Homo_sapiens.GRCh38.dna.toplevel.fa.gz hs.fa.gz
ln -s /work/data/homo_protein/ensemble/v102/Leptobrachium_leishanense.ASM966780v1.102.chr.gff3.gz ll.gff3.gz
ln -s /work/data/homo_protein/ensemble/v102/Leptobrachium_leishanense.ASM966780v1.dna.toplevel.fa.gz ll.fa.gz
ln -s /work/data/homo_protein/ensemble/v102/Mus_musculus.GRCm38.102.chr.gff3.gz mm.gff3.gz
ln -s /work/data/homo_protein/ensemble/v102/Mus_musculus.GRCm38.dna.toplevel.fa.gz mm.fa.gz
ln -s /work/data/homo_protein/ensemble/v102/Xenopus_tropicalis.Xenopus_tropicalis_v9.1.102.chr.gff3.gz xt.gff3.gz
ln -s /work/data/homo_protein/ensemble/v102/Xenopus_tropicalis.Xenopus_tropicalis_v9.1.dna.toplevel.fa.gz xt.fa.gz

agat_sp_filter_feature_by_attribute_value.pl --gff dr.gff3.gz --attribute biotype --value protein_coding -t '!' -o Danio_rerio.protein_coding.gff3
agat_sp_keep_longest_isoform.pl --gff Danio_rerio.protein_coding.gff3 -o Danio_rerio.longest_isoform.gff3

agat_sp_filter_feature_by_attribute_value.pl --gff hs.gff3.gz --attribute biotype --value protein_coding -t '!' -o Homo_sapiens.protein_coding.gff3
agat_sp_keep_longest_isoform.pl --gff Homo_sapiens.protein_coding.gff3 -o Homo_sapiens.longest_isoform.gff3

agat_sp_filter_feature_by_attribute_value.pl --gff ll.gff3.gz --attribute biotype --value protein_coding -t '!' -o Leptobrachium_leishanense.protein_coding.gff3
agat_sp_keep_longest_isoform.pl --gff Leptobrachium_leishanense.protein_coding.gff3 -o Leptobrachium_leishanense.longest_isoform.gff3

agat_sp_filter_feature_by_attribute_value.pl --gff mm.gff3.gz --attribute biotype --value protein_coding -t '!' -o Mus_musculus.protein_coding.gff3
agat_sp_keep_longest_isoform.pl --gff Mus_musculus.protein_coding.gff3 -o Mus_musculus.longest_isoform.gff3

agat_sp_filter_feature_by_attribute_value.pl --gff xt.gff3.gz --attribute biotype --value protein_coding -t '!' -o Xenopus_tropicalis.protein_coding.gff3
agat_sp_keep_longest_isoform.pl --gff Xenopus_tropicalis.protein_coding.gff3 -o Xenopus_tropicalis.longest_isoform.gff3

#GeMoMa 同源比对预测基因
java -jar /share/work/biosoft/GeMoMa/GeMoMa-1.9/GeMoMa-1.9.jar CLI GeMoMaPipeline
threads=200 AnnotationFinalizer.r=NO p=false o=true tblastn=false
t=contig.hardmasked.fa outdir=gemoma
s=own i=dr a=Danio_rerio.longest_isoform.gff3 g=dr.fa.gz
s=own i=hs a=Homo_sapiens.longest_isoform.gff3 g=hs.fa.gz
s=own i=ll a=Leptobrachium_leishanense.longest_isoform.gff3 g=ll.fa.gz
s=own i=mm a=Mus_musculus.longest_isoform.gff3 g=mm.fa.gz
s=own i=xt a=Xenopus_tropicalis.longest_isoform.gff3 g=xt.fa.gz

#转换数据
GeMoMa_gff_to_gff3.pl gemoma/final_annotation.gff > gemoma.evm.format.gff3

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Uploading 08.GeMoMa.sh.o.txt…

from jstacs.

Hi sujianed,

Thanks a lot for the information. Unfortunately, I'm not sure whether you still have the problems or whether you solved it.

I did not see the content of the output file:

Uploading 08.GeMoMa.sh.o.txt…
For me, this appears as a link to the issue.

best regards, Jens

from jstacs.

Hi sujianed,
any news from your side?
Could I close the issue?
best regards, Jens

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