Remove all unplaced scaffolds and contigs from the assemblies.

[NicMAlexandre]

I ran the following to generate a sam file:

minimap2 -ax asm20 --cs --eqx -t 20 reference.fa query.fna > query.sam

But when I run syri on the sam file:

syri/syri/bin/syri -c query.sam -r reference.fa -q query.fna -k -F S

I get the following warnings:

SAM reader - WARNING - Scaffold1 do not align with any reference sequence and cannot be analysed. Remove all unplaced scaffolds and contigs from the assemblies. ...........#repeated for many different scaffolds Reading Coords - WARNING - Chromosomes IDs do not match. Reading Coords - ERROR - Unequal number of chromosomes in the genomes. Exiting

[mnshgl0110]

Please check documentation https://schneebergerlab.github.io/syri/pipeline.html

[NicMAlexandre]

I understand now, i’ve been looking at a different tutorial that didn’t mention this. Thank you!