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Gaius-Augustus / GALBA

GALBA is a pipeline for fully automated prediction of protein coding gene structures with AUGUSTUS in novel eukaryotic genomes for the scenario where high quality proteins from one or several closely related species are available.
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warning: Coverage appears to be high, --ignoreCoverage flag will be ignored #35

Closed alexvasilikop closed 8 months ago

alexvasilikop commented 1 year ago

Hello,

While running GALBA version 1.0.6 using singularity the following warning is thrown:

$ singularity exec galba.sif galba.pl --genome=$genome --prot_seq=$proteins --threads 16 --gff3 --prg=miniprot --AUGUSTUS_ab_initio --species=species
# Mon Jun 19 11:21:26 2023: Log information is stored in file /mnt/sda1/Alex/09.GENOME_ANNOTATIONS/species/08.GALBA/GALBA/GALBA.log
warning: Coverage appears to be high, --ignoreCoverage flag will be ignored

Can this be safely ignored and what does it mean?

Many thanks Alex

KatharinaHoff commented 1 year ago

This means that only few redundant proteins were aligned to the majority of loci. Galba can work with e.g. only one reference set (from one species), it then throws the warning. It will achieve higher accuracy if you can provide protein sets of more close relatives. But that is sometimes impossible.

Alexandros Vasilikopoulos @.***> schrieb am Mo. 19. Juni 2023 um 11:47:

Hello,

While running GALBA version 1.0.6 using singularity the following warning is thrown:

$ singularity exec galba.sif galba.pl --genome=$genome --prot_seq=$proteins --threads 16 --gff3 --prg=miniprot --AUGUSTUS_ab_initio --species=species

Mon Jun 19 11:21:26 2023: Log information is stored in file /mnt/sda1/Alex/09.GENOME_ANNOTATIONS/species/08.GALBA/GALBA/GALBA.log

warning: Coverage appears to be high, --ignoreCoverage flag will be ignored

Cant this be safely ignored and what does it mean?

Many thanks Alex

— Reply to this email directly, view it on GitHub https://github.com/Gaius-Augustus/GALBA/issues/35, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJMC6JHQDLSPX34AUQ4MZ2DXMAN25ANCNFSM6AAAAAAZLVXRJE . You are receiving this because you are subscribed to this thread.Message ID: @.***>

alexvasilikop commented 1 year ago

Great thanks a lot,

I actually combined the proteins from 3 different species of the same genus in the same file (not sure however about their evolutionary distance but this is what I have available).

In any case the pipeline did not complete and I get the same error as mentioned in another thread #32:

# Mon Jun 19 11:46:16 2023: Log information is stored in file /mnt/sda1/Alex/09.GENOME_ANNOTATIONS/species/08.GALBA/GALBA/GALBA.log
warning: Coverage appears to be high, --ignoreCoverage flag will be ignored 
ERROR in file /opt/GALBA/scripts/galba.pl at line 5068
Failed to execute: /opt/conda/bin/python3 /mnt/sda1/Alex/09.GENOME_ANNOTATIONS/species/08.GALBA/GALBA/pygustus_hints.py 1> /mnt/sda1/Alex/09.GENOME_ANNOTATIONS/species/08.GALBA/GALBA/pygustus_hints.out 2>/mnt/sda1/Alex/09.GENOME_ANNOTATIONS/species/08.GALBA/GALBA/errors/pygustus_hints.err

Any help would be appreciated Thanks Alex

KatharinaHoff commented 11 months ago

Are there any hints in the hintsfile.gff ? I am wondering whether pygustus fails because we provide an empty hintsfile. (It shouldn't do that... but I since I didn't write pygustus, I am not sure)

alexvasilikop commented 10 months ago

Unfortunately I have deleted this dataset as i could not find the source of error; if i run again into the same problem I will post the results here

On Mon, Jun 19, 2023 at 12:14 PM Katharina Hoff @.***> wrote:

This means that only few redundant proteins were aligned to the majority of loci. Galba can work with e.g. only one reference set (from one species), it then throws the warning. It will achieve higher accuracy if you can provide protein sets of more close relatives. But that is sometimes impossible.

Alexandros Vasilikopoulos @.***> schrieb am Mo. 19. Juni 2023 um 11:47:

Hello,

While running GALBA version 1.0.6 using singularity the following warning is thrown:

$ singularity exec galba.sif galba.pl --genome=$genome --prot_seq=$proteins --threads 16 --gff3 --prg=miniprot --AUGUSTUS_ab_initio --species=species

Mon Jun 19 11:21:26 2023: Log information is stored in file

/mnt/sda1/Alex/09.GENOME_ANNOTATIONS/species/08.GALBA/GALBA/GALBA.log warning: Coverage appears to be high, --ignoreCoverage flag will be ignored

Cant this be safely ignored and what does it mean?

Many thanks Alex

— Reply to this email directly, view it on GitHub https://github.com/Gaius-Augustus/GALBA/issues/35, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AJMC6JHQDLSPX34AUQ4MZ2DXMAN25ANCNFSM6AAAAAAZLVXRJE>

. You are receiving this because you are subscribed to this thread.Message ID: @.***>

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-- Alexandros Vasilikopoulos Dr. rer. nat.

Postdoctoral researcher

Research unit of Molecular Biology and Evolution (MBE) Université libre de Bruxelles (ULB) Faculté des Sciences Campus du Solbosch Avenue F.D. Roosevelt, 50 1050 Bruxelles - BELGIUM