galba.gtf not created

[kullrich]

Hi I am running GALBA like this:

I have combined annotated proteins from three closely related species as protein hints.

galba.pl --genome=apo-wxms-hapog10-bionano-opera-final.fna --species=apodemus_uralensis --prot=GRCm39_mRatBN7.2_mApoSyl1.1_protein.faa --AUGUSTUS_ab_initio --gff3 --threads 48

and due to the log file it finished the pipeline:

Singularity> tail GALBA.log 
Deleting file /home/ullrich/projects/own_projects/assemblies/gene_annotation/galba/apo_hapog10/GALBA/genome.fa
Deleting file /home/ullrich/projects/own_projects/assemblies/gene_annotation/galba/apo_hapog10/GALBA/secondtest.stdout
Deleting file /home/ullrich/projects/own_projects/assemblies/gene_annotation/galba/apo_hapog10/GALBA/train.gb
Deleting file /home/ullrich/projects/own_projects/assemblies/gene_annotation/galba/apo_hapog10/GALBA/genome.fa.cidx
Deleting file /home/ullrich/projects/own_projects/assemblies/gene_annotation/galba/apo_hapog10/GALBA/getAnnoFastaFromJoingenes.augustus.hints_tmp.stdout
Deleting file /home/ullrich/projects/own_projects/assemblies/gene_annotation/galba/apo_hapog10/GALBA/traingenes.good.gtf
Deleting file /home/ullrich/projects/own_projects/assemblies/gene_annotation/galba/apo_hapog10/GALBA/genome.mpi
#**********************************************************************************
#                               GALBA RUN FINISHED                                
#**********************************************************************************

However, the galba.gtf file is missing in the end.

The files that have been produced are:

ls -alrt | awk '{print $9}'
genome_header.map
protein_alignment_miniprot.aln
miniprot.gff
miniprothint.gff
hc.gff
protein_alignment_miniprot.gff
hintsfile.gff
species
what-to-cite.txt
train2.gb
gff2gbSmallDNA.stderr
train2.gb.train
train2.gb.test
train2.gb.train.train
train2.gb.train.test
optimize_augustus.stdout
thirdtest.stdout
pygustus_ab_initio.py
augustus.abinitio.gff
pygustus_ab_initio.out
augustus.abinitio.tmp.gtf
augustus.abinitio.gtf
augustus.abinitio.codingseq
augustus.abinitio.aa
getAnnoFastaFromJoingenes.augustus.abinitio_tmp.stdout
pygustus_hints.py
augustus.hints.gff
pygustus_hints.out
augustus.hints.gtf
augustus.hints.codingseq
augustus.hints.aa
augustus.hints.gff3
errors
.
GALBA.log

Is the augustus.hints.gff3 file the actual final output file in this case?

Best regards

Kristian

[KatharinaHoff]

Thanks for pointing this out. I now realize that I need to fix something in the GALBA code.

For now, the augustus.hints.gtf file of your job is the output, that's correct. But I should implement a copy or softlink process.

[yuzhenpeng]

Hi @KatharinaHoff

I met the same problem. Do you solved it？

[KatharinaHoff]

It looks like it is solved with the latest release. When I run test1.sh (with added --gff3 flag), I get the following output:

archive errors galba.aa galba.codingseq galba.gff3 galba.gtf GALBA.log genome_header.map hintsfile.gff species what-to-cite.txt

(I also moved a few files that I prefer not to delete but that are less important to many users to a folder archive)