This error occurs because there is something wrong with the gff file.

[08li20]

Run the command as follows：vg autoindex --threads 2 --workflow mpmap --prefix cattle --ref-fasta Cattle_ARS-UCD2.0_GCF_002263795.3_rename.fa --vcf cattle.variants.vcf --tx-gff cattle.trans.gff

error:[IndexRegistry] contig 1 RefSeq region 1 158534110 . + . ID=NC_037328.1:1..158534110;Dbxref=taxon:9913;Name=1;breed=Hereford;chromosome=1;gbkey=Src;genome=chromosome;isolate=L1;Dominette;01449;registration;number;42190680;mol_type=genomic;DNA;sex=female;tissue-type=left;lung from GTF/GFF cattle.trans.gff is not found in reference

[jeizenga]

It looks to me like the entire GFF line is being parsed as its contig name. Maybe the GFF you have is space-separated instead of tab-separated?

[08li20]

After converting the delimiter character in the gff file to tab character, an error message is still reported saying that it cannot be found in the reference sequence. vg autoindex --threads 2 --workflow mpmap --prefix cattle --ref-fasta Cattle_ARS-UCD2.0_GCF_002263795.3_rename.fa --vcf cattle.variants.vcf --tx-gff cattle.gff error:[IndexRegistry] contig 1 from GTF/GFF cattle.gff is not found in reference

[08li20]

Will the lack of comment lines in the gff file affect the matching?

[jeizenga]

No, it would not. My guess is that it's most likely a "1" vs "chr1" mismatch. If not that, then some other mismatched representation. You can get a quick look at the sequence names in the FASTA with grep ">" ref.fa, which will probably make the source of the error obvious.

[08li20]

I changed the chromosome names in the reference genome and the chromosome names in the gff file to be the same, but the same error still occurred. vg autoindex --threads 2 --workflow mpmap --prefix cattle --ref-fasta Cattle_ARS-UCD2.0_GCF_002263795.3_rename.fa --vcf cattle.variants.vcf --tx-gff cattle.gff2 error:[IndexRegistry] contig >1 from GTF/GFF cattle.gff2 is not found in reference

[jeizenga]

The GFF now appears to have the > from the FASTA name line inserted into the contig name, so I think this was probably a move in the wrong direction. Can you copy the output of these commands? Then I can probably be more specific.

grep ">" Cattle_ARS-UCD2.0_GCF_002263795.3_rename.fa | head

and

head cattle.gff2

[08li20]

After I modified the gff file, I ran the following command, but ERROR: Tag "transcript_id" not found in attributes (line 145).ERROR: Tag "transcript_id" not found in attributes (line 4).ERROR: No transcripts parsed (remember to set feature type "-y" in vg rna or "-f" in vg autoindex error, here is how to change the -f parameter in vg autoindex specifically vg autoindex --threads 5 --workflow mpmap --prefix cattle --ref-fasta Cattle_ARS-UCD2.0_GCF_002263795.3_rename.fa --vcf cattle.variants.vcf --tx-gff cattlecattle.gff5

ERROR: Tag "transcript_id" not found in attributes (line 145). ERROR: Tag "transcript_id" not found in attributes (line 4). ERROR: No transcripts parsed (remember to set feature type "-y" in vg rna or "-f" in vg autoindex)

[jeizenga]

Typically, a GFF file will include a unique identifier for each transcript as annotations in column 9. Often it's an accession number from a public database. Different genome annotation projects use different labels for the identifier, so you have to specify which one is the unique identifier using the --gff-tx-tag argument. The default transcript_id is what's used by GENCODE, but you'll have to figure out what the label is in your data set.

[08li20]

The command reported an error saying that transcript_id was not detected in line 145 of the gff file, but line 145 of my file was commented as CDS, and I added the parameter --gff-feature exon to only recognize the exon in the third line of the gff file. vg autoindex --threads 5 --gff-feature exon --gff-tx-tag transcript_id --workflow mpmap --prefix cattle --ref-fasta Cattle_ARS-UCD2.0_GCF_002263795.3_rename.fa --vcf cattle.variants.vcf --tx-gff cattlecattle.gff5 ERROR: Tag "transcript_id" not found in attributes (line 145).

[jeizenga]

Can you send the GFF file you're using?

[08li20]

sam.gff.docx This is the content of the first two hundred lines of the gff file

[jeizenga]

Closing here since you have opened the same thing as a separate issue at https://github.com/vgteam/vg/issues/4264