gatech-genemark/ProtHint
Protein hint generation pipeline for gene finding in eukaryotic genomes
PythonNOASSERTION
Issues
- 2
The hints file(s) for GeneMark-EX contain less than 150 introns with multiplicity >= 4!
#60 opened by yzliu01 - 7
- 7
Could not find gmes_petap.pl in the PATH
#58 opened by karthickbrlab - 1
Addition of iso-seq data
#57 opened by ardy20 - 9
Preparation of database from OrthoDB
#39 opened by dariober - 1
genemark_hintsfile.gff.rnaseq.tmp': No such file or directory, ERROR Failed to execute: mv
#56 opened by kinoppyi - 1
Freeze at 99,9%
#55 opened by tberthelier - 3
- 6
Error: file not found
#53 opened by kdarragh1994 - 1
set.out error?
#54 opened by mabh5 - 1
How to access relevant portion of OrthoDB v11
#52 opened by xiekunwhy - 1
GeneMark-ES, can't locate YAML.pm module
#51 opened by tzaquin - 12
ProtHint license question
#6 opened by npavlovikj - 12
proteins_from_gtf.pl issue
#49 opened by francesco-ricci - 1
alternative start codons
#48 opened by cpaight - 6
No unique gene seeds were detected
#36 opened by tinyfallen - 10
file not found: data/training.fna
#42 opened by miferg - 1
number of threads ::
#46 opened by EricDeveaud - 1
number of threads
#47 opened by EricDeveaud - 5
- 1
- 2
prothint_augustus.gff used for augustus training
#40 opened by hrluo93 - 1
- 2
- 1
Error in braker (Prothint step)
#38 opened by minhasbushra - 5
Protein database preparation
#37 opened by minhasbushra - 5
error, file not found parse_set.pl: set.out
#35 opened by mictadlo - 6
No prothint_augustus.gff output
#34 opened by peritob - 2
which one should l use?
#32 opened by ld9866 - 2
Which database should I use
#33 opened by ld9866 - 1
Incomplete output
#25 opened by dianamosa - 1
Genome is softmasked?
#29 opened by pjx1990 - 2
- 2
grep -P fails in Biocontainers image
#27 opened by nathanweeks - 9
No homologous proteins were found by DIAMOND
#26 opened by Huangyizhong - 3
shell errors? -- grep topProt=TRUE Spaln/spaln.gff > topProteins.gff || [[ $? == 1 ]]
#18 opened by conchoecia - 2
- 5
- 0
- 9
Error, file not found
#5 opened by br302005 - 1
- 3
ProtHint hanging at 99.9% during alignment
#14 opened by tkjmk - 1
error: Alignment is missing after header
#16 opened by PeiwenLi - 5
ProtHint exited due to an error in command: grep Intron Spaln/spaln.gff > introns.gff
#15 opened by lfaller-zymergen - 8
No stop codons in spaln.gff
#13 opened by cdmmoeller - 2
GeneMark page is currently down
#12 opened by mauriciolangleib - 4
Speed of the process
#9 opened by skyungyong - 0
- 1
Option to redirect all output to file
#4 opened by KatharinaHoff - 2
Number of threads inconsistent?
#3 opened by KatharinaHoff