Pigeon classify error: error loading reference annotations for reference; vector::reserve

[SidG13]

Hi,

I'm trying to figure out exactly what's wrong with my GTF when running pigeon classify, because it seemingly processes the first 7 chromosomes correctly, but something is wrong with the 8th. I've isolated the problem to any chromosome named "scaffold-mi*", where the "*" represents a number (when I remove scaffold-mi1 from the GTF, it fails at scaffold-mi2). But the GTF lines are identical in structure across the GTF, so I'm completed lost as to why this is happening. This is a GTF specifically modified to work with the IsoSeq pipeline, but otherwise I've been using the original GTF for a long time for many other applications, and the chromosomes do exist in the genome fasta, names match.

The GTF file sorted and indexed fine using pigeon prepare, so no issues there. The GTF was formatted as a standard 9 column file as well, with gene_id, transcript_id and gene_name in the 9th column.

Here's a screenshot of the problematic lines.

The exact command structure I ran is:

pigeon classify sample.collapsed.sorted.gff sample.reference.pigeon.sorted.gtf genome.fa

Basically, pigeon classify works on seven chromosomes, then drops the following error:

| 20240916 20:18:14.118 | FATAL | pigeon classify ERROR: error loading reference annotations for reference: scaffold-mi1 vector::reserve.

Separately, I used agat_convert_sp_gff2gtf.pl to check for errors in formatting. The GTF produced by AGAT also had the same issue at scaffold-mi1.

Any guidance is appreciated!

I've attached my .pgi GTF reference file in case that may help.
CroVir_rnd1.all.maker.final.homologIDs.updatedNov2019_with_myos_geneidmod_pigeon.sorted.gtf.pgi.txt

Some version details:

pigeon --version
pigeon 1.2.0 (commit -v1.2.0)

Using:
  pbbam     : 2.5.0 (commit v2.5.0)
  pbcopper  : 2.4.0 (commit v2.4.0)
  boost     : 1.81
  htslib    : 1.17
  zlib      : 1.2.13