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Error - Reading Coords - WARNING - Chromosomes IDs do not match. Unequal number of chromosomes in the genomes. #295
Description
Hi,
I assembled a genome with PacBio reads, and then my PI asked a company, Cantata Bio, to use Hi-C data to scaffold it. Thus it changes from 203 contigs to 176 scaffolds. Oddly, the company reported 2 breaks and 1 join, which don't match the data since the differences based on the number of contigs/scaffolds it way higher.
I wanted to use syri to identify structural variants, and I first did whole-genome assembly alignment with minimap:
minimap2 -ax asm5 -t 48 -K 10G --eqx final_assembly.fasta /HydLep.f1x.fasta > out.sam
For some reason, minimap2 didn't work at first but somehow I made it work, and I got the output, but then
when running syri, I got the error:
Reading Coords - WARNING - Chromosomes IDs do not match.
Reading Coords - ERROR - Unequal number of chromosomes in the genomes. Exiting
I used this code:
syri -c out.sam -r final_assembly.fasta -q HydLep.f1x.fasta -k -F S --nc 48 --nosnp
Because the company scaffolded the genome and the number of contigs is less they have different names obviously. The names can't and shouldn't be the same.
Any reason why this weird error?
Activity
lrauschning commentedon Dec 2, 2025
Hi @desmodus1984 ,
sorry for the late answer, for some reason I only got the notification for this issue just now.
SyRI is a tool for working with chromosome-scale assemblies. I'm assuming your species has fewer than 176 chromosomes, so your assembly is not chromosome scale, and thus SyRI reports the different no of contigs as mismatching chromosomes.
I'm not sure why the company's scaffolding seems to have been so incomplete; you can try it yourself using GreenHill or AllHiC (if you're working in polyploids) or any of the other tools for this out there if your HiC data is sufficient.
Otherwise, you may try reference based scaffolding using e.g. RagTag, though be warned that this may overcorrect some structural variants during the scaffolding step in fragmented assemblies like yours.
Another note of caution, we've observed that minimap2 can behave a bit weirdly in very repetitive and diverse plant genomes. Definitely take a look at your alignments if your species fits that bill, and try playing around with alignment parameters and/or different aligners.
I hope that helps!
Cheers,
Leon
Nitin123-4 commentedon Jan 30, 2026
Synteny we would like to do based on one reference genome and any other query genome, Whatever is the chromosome/Scaffold ids are. It should Ideally support it. If possible please add support for this.