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Gaius-Augustus / BRAKER

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes
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error: No spliced alignments were created by Spaln #793

Closed karthickbrlab closed 2 months ago

karthickbrlab commented 3 months ago

I just used proteins from arabidopsis thaliana in --prot.seq.

error: No spliced alignments were created by Spaln (/home/ubuntu/BRAKER/scripts/braker/Spaln/spaln.gff is empty). This error can be caused by: a) The set of input proteins is too small and/or the proteins are too remote. b) The gene seeds identified by GeneMark-ES (or the supplied gene seeds in case the option "--geneSeeds" was used) are incorrect. Please try running GeneMark-ES separately to identify errors related to gene seeds (https://github.com/gatech-genemark/ProtHint#genemark-es).

tanpham15 commented 3 months ago

Hi,

I also got this error message. I used proteins database for Arthropoda.gz. Moreover, I rerun GeneMark separately, but I didn't find any error (please check the gmes.log and gmetp.sh.o3447546 for detail)

Best regards, Tan

karthickbrlab commented 2 months ago

hi,

I rerun with Viridiplantae proteins.gz, still getting this error.

cat: nuc_2091718_prot_2091718: No such file or directory rm: cannot remove 'nuc_2091718_prot_2091718': No such file or directory /home/ubuntu/deru/Deru_data/genemark/ProtHint/spalnBatch.sh: line 61: /home/ubuntu/deru/Deru_data/genemark/ProtHint/../dependencies/spaln_boundary_scorer: No such file or directory cat: nuc_2091719_prot_2091719: No such file or directory rm: cannot remove 'nuc_2091719_prot_2091719': No such file or directory [Thu Apr 4 09:58:25 2024] 2091719/2091719 (100%) pairs aligned [Thu Apr 4 09:58:25 2024] Alignment of pairs finished [Thu Apr 4 09:58:25 2024] Translating coordinates from local pair level to contig level [Thu Apr 4 09:58:28 2024] Finished spliced alignment error: No spliced alignments were created by Spaln (/home/ubuntu/BRAKER/scripts/braker/Spaln/spaln.gff is empty).

This error can be caused by: a) The set of input proteins is too small and/or the proteins are too remote. b) The gene seeds identified by GeneMark-ES (or the supplied gene seeds in case the option "--geneSeeds" was used) are incorrect. Please try running GeneMark-ES separately to identify errors related to gene seeds (https://github.com/gatech-genemark/ProtHint#genemark-es).

ERROR in file braker.pl at line 5355 Failed to execute /home/ubuntu/genemark/ProtHint/prothint.py --threads=1 --geneMarkGtf /home/ubuntu/BRAKER/scripts/braker/GeneMark-ES/genemark.gtf /home/ubuntu/BRAKER/scripts/braker/genome.fa /home/ubuntu/BRAKER/scripts/braker/proteins.fa!

karthickbrlab commented 2 months ago

Im closing this issue.

Worked well after reinstallation

Thanks for your assistance