GeMoMa error #53
Comments
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Hi sujianed, thanks a lot for your interest in GeMoMa. I would be happy to help you. 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 but,When I use animal Danio_rerio, Homo_sapiens, Leptobrachium_leishanense, Mus_musculus, Xenopus_tropicalis, it's not OK Oddly enough, when I use "java -jar /share/work/biosoft/GeMoMa/GeMoMa-1.9/GeMoMa-1.9.jar CLI GeMoMaPipeline "java -jar /share/work/biosoft/GeMoMa/GeMoMa-1.9/GeMoMa-1.9.jar CLI GeMoMaPipeline |
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Hi sujianed, I'm sorry that you still have problems and it is hard for me to follow. However, I realized
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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################################## mkdir 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 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_filter_feature_by_attribute_value.pl --gff hs.gff3.gz --attribute biotype --value protein_coding -t '!' -o Homo_sapiens.protein_coding.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_filter_feature_by_attribute_value.pl --gff mm.gff3.gz --attribute biotype --value protein_coding -t '!' -o Mus_musculus.protein_coding.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 #GeMoMa 同源比对预测基因 #转换数据 |
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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:
best regards, Jens |
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Hi sujianed, |
code:
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
s=own i=xt a=Xenopus_tropicalis.longest_isoform.gff3 g=xt.fa.gz
error:Searching for the new GeMoMa updates ...
You are using the latest GeMoMa version.
Parameters of tool "GeMoMa pipeline" (GeMoMaPipeline, version: 1.9):
t - target genome (Target genome file (FASTA), type = fasta,fa,fas,fna,fasta.gz,fa.gz,fas.gz,fna.gz) = contig.hardmasked.fa
The following parameter(s) can be used multiple times:
s (1) - species (data for reference species, range={own, pre-extracted}, default = own) = own
Parameters for selection "own":
i (1) - ID (ID to distinguish the different reference species, OPTIONAL) = ll
a (1) - annotation (Reference annotation file (GFF or GTF), which contains gene models annotated in the reference genome, type = gff,gff3,gtf,gff.gz,gff3.gz,gtf.gz) = Leptobrachium_leishanense.longest_isoform.gff3
g (1) - genome (Reference genome file (FASTA), type = fasta,fa,fas,fna,fasta.gz,fa.gz,fas.gz,fna.gz) = ll.fa.gz
w (1) - weight (the weight can be used to prioritize predictions from different input files; each prediction will get an additional attribute sumWeight that can be used in the filter, valid range = [0.0, 1000.0], default = 1.0, OPTIONAL) = 1.0
ai (1) - annotation info (annotation information of the reference, tab-delimted file containing at least the columns transcriptName, GO and .*defline, type = tabular, OPTIONAL) = null
Parameters for selection "pre-extracted":
i (1) - ID (ID to distinguish the different reference species, OPTIONAL) = null
c (1) - cds parts (The query CDS parts file (protein FASTA), i.e., the CDS parts that have been searched in the target genome using for instance BLAST or mmseqs, type = fasta,fa,fas,fna) = null
a (1) - assignment (The assignment file, which combines CDS parts to proteins, type = tabular, OPTIONAL) = null
w (1) - weight (the weight can be used to prioritize predictions from different input files; each prediction will get an additional attribute sumWeight that can be used in the filter, valid range = [0.0, 1000.0], default = 1.0, OPTIONAL) = 1.0
ai (1) - annotation info (annotation information of the reference, tab-delimited file containing at least the columns transcriptName, GO and .*defline, type = tabular, OPTIONAL) = null
s (2) - species (data for reference species, range={own, pre-extracted}, default = own) = own
Parameters for selection "own":
i (2) - ID (ID to distinguish the different reference species, OPTIONAL) = mm
a (2) - annotation (Reference annotation file (GFF or GTF), which contains gene models annotated in the reference genome, type = gff,gff3,gtf,gff.gz,gff3.gz,gtf.gz) = Mus_musculus.longest_isoform.gff3
g (2) - genome (Reference genome file (FASTA), type = fasta,fa,fas,fna,fasta.gz,fa.gz,fas.gz,fna.gz) = mm.fa.gz
w (2) - weight (the weight can be used to prioritize predictions from different input files; each prediction will get an additional attribute sumWeight that can be used in the filter, valid range = [0.0, 1000.0], default = 1.0, OPTIONAL) = 1.0
ai (2) - annotation info (annotation information of the reference, tab-delimted file containing at least the columns transcriptName, GO and .*defline, type = tabular, OPTIONAL) = null
Parameters for selection "pre-extracted":
i (2) - ID (ID to distinguish the different reference species, OPTIONAL) = null
c (2) - cds parts (The query CDS parts file (protein FASTA), i.e., the CDS parts that have been searched in the target genome using for instance BLAST or mmseqs, type = fasta,fa,fas,fna) = null
a (2) - assignment (The assignment file, which combines CDS parts to proteins, type = tabular, OPTIONAL) = null
w (2) - weight (the weight can be used to prioritize predictions from different input files; each prediction will get an additional attri
...skipping...
java.lang.InterruptedException
at java.base/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.reportInterruptAfterWait(AbstractQueuedSynchronizer.java:2056)
at java.base/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2133)
at java.base/java.util.concurrent.ThreadPoolExecutor.awaitTermination(ThreadPoolExecutor.java:1454)
at projects.gemoma.GeMoMaPipeline$1.run(GeMoMaPipeline.java:609)
at projects.gemoma.GeMoMaPipeline$FlaggedRunnable.run(GeMoMaPipeline.java:1409)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:834)
GeMoMa for species 0 (ll) split=114 throws an Exception
GeMoMa for species 1 (mm) split=25 throws an Exception
GeMoMa for species 0 (ll) split=108 throws an Exception
GeMoMa for species 1 (mm) split=3 throws an Exception
java.lang.InterruptedException
at java.base/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.reportInterruptAfterWait(AbstractQueuedSynchronizer.java:2056)
at java.base/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2133)
at java.base/java.util.concurrent.ThreadPoolExecutor.awaitTermination(ThreadPoolExecutor.java:1454)
at projects.gemoma.GeMoMaPipeline$1.run(GeMoMaPipeline.java:609)
at projects.gemoma.GeMoMaPipeline$FlaggedRunnable.run(GeMoMaPipeline.java:1409)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:834)
GeMoMa for species 0 (ll) split=196 throws an Exception
GeMoMa for species 1 (mm) split=31 throws an Exception
GeMoMa for species 1 (mm) split=10 throws an Exception
GeMoMa for species 1 (mm) split=90 throws an Exception
GeMoMa for species 1 (mm) split=99 throws an Exception
GeMoMa for species 0 (ll) split=10 throws an Exception
GeMoMa for species 0 (ll) split=85 throws an Exception
GeMoMa for species 1 (mm) split=57 throws an Exception
GeMoMa for species 0 (ll) split=113 throws an Exception
GeMoMa for species 0 (ll) split=153 throws an Exception
Error, cannot open file gemoma/final_annotation.gff at /share/work/biosoft/EVidenceModeler/latest/EvmUtils/misc/GeMoMa_gff_to_gff3.pl line 23.
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