gatech-genemark ProtHint issues

gatech-genemark / ProtHint

Protein hint generation pipeline for gene finding in eukaryotic genomes

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issues

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The hints file(s) for GeneMark-EX contain less than 150 introns with multiplicity >= 4!

#60 yzliu01 opened 3 months ago
2
error: No spliced alignments were created by Spaln

#59 karthickbrlab closed 5 months ago
7
Could not find gmes_petap.pl in the PATH

#58 karthickbrlab closed 7 months ago
7
Addition of iso-seq data

#57 ardy20 closed 7 months ago
1
genemark_hintsfile.gff.rnaseq.tmp': No such file or directory, ERROR Failed to execute: mv

#56 kinoppyi opened 1 year ago
1
Freeze at 99,9%

#55 tberthelier opened 1 year ago
1
set.out error?

#54 mabh5 closed 1 year ago
1
Error: file not found

#53 kdarragh1994 opened 1 year ago
6
How to access relevant portion of OrthoDB v11

#52 xiekunwhy closed 1 year ago
1
GeneMark-ES, can't locate YAML.pm module

#51 tzaquin closed 1 year ago
1
petap.pl fails on one sample but not others, too few introns

#50 ToriEggers opened 1 year ago
3
proteins_from_gtf.pl issue

#49 francesco-ricci closed 2 years ago
12
alternative start codons

#48 cpaight opened 2 years ago
1
number of threads

#47 EricDeveaud closed 2 years ago
1
number of threads ::

#46 EricDeveaud closed 2 years ago
1
Error: Error detecting input file format. First line seems to be blank.

#45 qussai96 closed 2 years ago
5
Issues with running example file: CPU does not support SSSE3

#44 HitMonk closed 2 years ago
1
Error: ProtHint/ACAB/prothint_augustus.gff not found !

#43 CongLiu37 opened 2 years ago
1
file not found: data/training.fna

#42 miferg closed 2 years ago
10
Generate ProtHint seed regions without GeneMark-ES

#41 CuriousTim closed 2 years ago
2
prothint_augustus.gff used for augustus training

#40 hrluo93 closed 2 years ago
2
Preparation of database from OrthoDB

#39 dariober closed 1 year ago
9
Error in braker (Prothint step)

#38 minhasbushra opened 2 years ago
1
Protein database preparation

#37 minhasbushra closed 2 years ago
5
No unique gene seeds were detected

#36 tinyfallen closed 2 years ago
6
error, file not found parse_set.pl: set.out

#35 mictadlo opened 2 years ago
5
No prothint_augustus.gff output

#34 peritob closed 3 years ago
6
Which database should I use

#33 ld9866 closed 3 years ago
2
which one should l use?

#32 ld9866 closed 3 years ago
2
spalnBatch.sh: increase spaln -l value so alignments don't span multiple lines

#31 nathanweeks closed 3 years ago
2
spaln_boundary_scorer and probuild not working in Braker2 Biocontainer

#30 qisun2 closed 3 years ago
2
Genome is softmasked?

#29 pjx1990 closed 3 years ago
1
Add support for predicting non-canonical introns

#28 tomasbruna closed 3 years ago
0
grep -P fails in Biocontainers image

#27 nathanweeks closed 3 years ago
2
No homologous proteins were found by DIAMOND

#26 Huangyizhong closed 3 years ago
9
Incomplete output

#25 dianamosa closed 3 years ago
1
Remove ProSplign-related code

#24 tomasbruna closed 3 years ago
0
Fix translation of partial seed genes

#23 tomasbruna closed 3 years ago
0
Continue when gft files start with comments

#22 monsanto-pinheiro closed 3 years ago
1
Prothint version2.5.0 cann't output evidence_augustus.gff file

#21 18616831168 closed 3 years ago
2
Recommended run parameters downstream for braker

#20 conchoecia closed 3 years ago
5
Enforce bash in system calls

#19 tomasbruna closed 3 years ago
0
shell errors? -- grep topProt=TRUE Spaln/spaln.gff > topProteins.gff || [[ $? == 1 ]]

#18 conchoecia closed 3 years ago
3
A bug (or feature...) in script 'bin/proteins_from_gtf.pl'

#17 TypicalSEE closed 3 years ago
1
error: Alignment is missing after header

#16 PeiwenLi closed 4 years ago
1
ProtHint exited due to an error in command: grep Intron Spaln/spaln.gff > introns.gff

#15 lfaller-zymergen closed 4 years ago
5
ProtHint hanging at 99.9% during alignment

#14 tkjmk closed 4 years ago
3
No stop codons in spaln.gff

#13 cdmmoeller opened 4 years ago
8
GeneMark page is currently down

#12 mauriciolangleib closed 4 years ago
2
Parallel speedup

#11 tomasbruna closed 4 years ago
0