Reading Coords - WARNING - Chromosomes IDs do not match.

[renmiaozhen]

I know this question has been asked for many times, but I try those solutions, it doesn't work.

The two genomes share homologous, but their homologous chromosome IDs don't match (such as chr1 homologous with chr6). See the picture as follows:

So, I renamed the chrIDs to make them match for subsequent analysis. At the same time, between these two genomes, their chrs were reversed strands like the picture shows. Thus, I use seqkit seq -r to reverse the strand direction. After preparing these, I follow the instructions normally until I run Syri. I received the Syri error info: Reading Coords - WARNING - Chromosomes IDs do not match. Reading Coords - ERROR - Unequal number of chromosomes in the genomes. Exiting

I don't know how to fix these errors, would you be able to help me?

[mnshgl0110]

Does any of the genomes contain contigs/scaffolds? Removing them should solve this.

[renmiaozhen]

Does any of the genomes contain contigs/scaffolds? Removing them should solve this.

My genomes have no contigs/scaffolds

[mnshgl0110]

How many DNA molecules are there in the reference and query genome fasta files? You can check that using using : grep -c '>' [REFERENCE].fasta

[renmiaozhen]

How many DNA molecules are there in the reference and query genome fasta files? You can check that using using : grep -c '>' [REFERENCE].fasta

I check my fasta file using grep -c '>' [REFERENCE].fasta , they are same.

[mnshgl0110]

This error happens when there are different number of chromosomes with informative alignments. If the genomes have same number of sequences, then the issue can happen if: 1) not all sequences (in both reference and query) are aligned: you can check the alignment file for this 2) for one (or more) sequence, all alignments are low quality and filtered out by syri: you can use syri's -f parameter to stop alignment filtering

[renmiaozhen]

This error happens when there are different number of chromosomes with informative alignments. If the genomes have same number of sequences, then the issue can happen if:

1. not all sequences (in both reference and query) are aligned: you can check the alignment file for this
2. for one (or more) sequence, all alignments are low quality and filtered out by syri: you can use syri's -f parameter to stop alignment filtering

OK, thank your answer.