updategff issues

[El-Castor]

Hi !

I have correct and scaffold my assembly regarding a close reference genome already sequenced. Now I am trying to update my gff from my no correcting assembly to the scaffolded one.

I have scafold my assembly using this command :

ragtag.py scaffold $geneome_faste_ref_DIR $outDir/ragtag.correct.fasta -o $outDir_scaffolding -t 16 -C

with

geneome_faste_ref_DIR: path to my genome of reference
outDir/ragtag.correct.fasta: path to my assembly corrected first
outDir_scaffolding: output directory

Then I try to update my gff following this command:

ragtag.py updategff $gff_PATH $current_agpScafolded_PATH

with:
gff_PATH: The gff file produce with augustus and related to my non corrected/scafold assembly (query)
current_agpScafolded_PATH: AGP ouput file from the ragtag.py scaffold command

Running this command I have an issue:

(ragtag) cpichot@node13:/NetScratch/FLOCAD/cpichot/genome_assembling/P.sativum_DGL_genomeAssembly$ ragtag.py updategff $gff_PATH_TEST $current_agpScafolded_PATH_TEST
Mon Jul 31 16:09:21 2023 --- VERSION: RagTag v2.1.0
Mon Jul 31 16:09:21 2023 --- CMD: ragtag.py updategff /NetScratch/FLOCAD/cpichot/genome_assembling/P.sativum_DGL_genomeAssembly/dgl_contigOfInterestOnly.20230210.gff3 /NetScratch/FLOCAD/cpichot/genome_assembling/1-improveAssembly/out-ragtag-Allgenome/ragtag.correct.agp
##gff-version 3
##sequence-region ptg000001l 1 642050

ptg000001l	BioFileConverter	gene	13645	14031	.	+	.ID=gene:ptg000001l.1;Name=ptg000001l.1;locus_tag=Ps_ptg000001lg000010
Traceback (most recent call last):
 File "/NetScratch/cpichot/.conda/envs/ragtag/bin/ragtag_update_gff.py", line 162, in <module>
   main()
 File "/NetScratch/cpichot/.conda/envs/ragtag/bin/ragtag_update_gff.py", line 156, in main
   sup_update(gff_file, agp_file)
 File "/NetScratch/cpichot/.conda/envs/ragtag/bin/ragtag_update_gff.py", line 114, in sup_update
   raise ValueError("Inconsistent input files.")

here you have a head of the AGP file:

## agp-version 2.1
# AGP created by RagTag v2.1.0
chr1LG6_RagTag	1	134342	1	W	ptg002004l_431067_565408_+	1	134342	+
chr1LG6_RagTag	134343	134442	2	U	100	scaffold	yes	align_genus
chr1LG6_RagTag	134443	177232	3	W	ptg002087l_457179_499968_+	1	42790	+
chr1LG6_RagTag	177233	177332	4	U	100	scaffold	yes	align_genus
chr1LG6_RagTag	177333	232767	5	W	ptg001609l_360920_416354_+	1	55435	+
chr1LG6_RagTag	232768	232867	6	U	100	scaffold	yes	align_genus
chr1LG6_RagTag	232868	300311	7	W	ptg002004l_1_67444_+	1	67444	+
chr1LG6_RagTag	300312	300411	8	U	100	scaffold	yes	align_genus

Do you see my mistake ? What should I do to correct this issue please?

Thanks in advance!