Describe the issue
Hello, I'm attempting to run VEP on a GFF created from scBUSCO genes. I consistently have issues with the command failing, when I remove the offending variant another takes its place. I know this issue is likely due to the format of my GFF as indicated in Issues #1074 #1615 and #1620 . I'm suspecting it's the lack of transcripts in the GFF. However, how best to modify my GFF to include this information at the scale that is necessary is a little overwhelming. Below is information for how the GFF was prepared after running BUSCO. A subset of the GFF is provided, and I can add the relevant VCF subset if needed.
Many thanks for your help and advice!
GFF file preparation
busco --in genome.fa --out busco/ --mode genome --lineage_dataset aves_odb10 --cpu 32
cat busco/run_aves_odb10/busco_sequences/single_copy_busco_sequences/*.gff > merged_scBUSCOs.gff
agat_sp_manage_IDs.pl --gff merged_scBUSCO.gff -o merged_scBUSCO_checked.gff
grep -v "#" merged_scBUSCOs_checked.gff | sort -k1,1 -k4,4n -k5,5n -t$'\t' | bgzip -c > merged_scBUSCOs_checked.gff.gz
tabix -p gff merged_scBUSCOs_checked.gff.gz
System
- VEP Versions (conda install):
ensembl: 115.266b84d
ensembl-compara: 115.ae48a7a
ensembl-funcgen: 115.57f7061
ensembl-io: 115.25061d3
ensembl-variation: 115.b7c2637
ensembl-vep: 115.2
- Perl version:
- OS: WSL
- tabix: v1.21
Full VEP command line
vep -i GLOBAL_polarized_variable.vcf \
--custom file=merged_scBUSCOs_checked.gff.gz,short_name=scBUSCOs,format=gff,type=overlap \
--fasta genome.fa \
-o SNP_vep.vcf --vcf --force_overwrite
Full error message
WARNING: Setting offline mode. To create database connection use either --database or --cache.
substr outside of string at /home/jwold/miniforge3/envs/vep/share/ensembl-vep-115.2-1/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 2340, <ANONIO> line 177373.
Can't call method "seq" on an undefined value at /home/jwold/miniforge3/envs/vep/share/ensembl-vep-115.2-1/Bio/EnsEMBL/Transcript.pm line 828, <ANONIO> line 646513.
BUSCO_subset.gff.gz
Describe the issue
Hello, I'm attempting to run VEP on a GFF created from scBUSCO genes. I consistently have issues with the command failing, when I remove the offending variant another takes its place. I know this issue is likely due to the format of my GFF as indicated in Issues #1074 #1615 and #1620 . I'm suspecting it's the lack of transcripts in the GFF. However, how best to modify my GFF to include this information at the scale that is necessary is a little overwhelming. Below is information for how the GFF was prepared after running BUSCO. A subset of the GFF is provided, and I can add the relevant VCF subset if needed.
Many thanks for your help and advice!
GFF file preparation
System
ensembl: 115.266b84d
ensembl-compara: 115.ae48a7a
ensembl-funcgen: 115.57f7061
ensembl-io: 115.25061d3
ensembl-variation: 115.b7c2637
ensembl-vep: 115.2
Full VEP command line
Full error message
WARNING: Setting offline mode. To create database connection use either --database or --cache.
substr outside of string at /home/jwold/miniforge3/envs/vep/share/ensembl-vep-115.2-1/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 2340, <ANONIO> line 177373.
Can't call method "seq" on an undefined value at /home/jwold/miniforge3/envs/vep/share/ensembl-vep-115.2-1/Bio/EnsEMBL/Transcript.pm line 828, <ANONIO> line 646513.
BUSCO_subset.gff.gz