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schneebergerlab / syri

Synteny and Rearrangement Identifier
https://schneebergerlab.github.io/syri/
MIT License
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syri reported an error:Reading coords - ERROR - aDir can only have values 1 #211

Closed zzzzzzzy7 closed 10 months ago

zzzzzzzy7 commented 10 months ago

Hi! According to the following code, I compared the two genomes with mummer to get out.delta, processed them with syri to get filter and coords file, and then tested sv with syri to get the error: Reading coords - ERROR - aDir can only have values 1.

nucmer --mum -c 100 -b 500 -l 50 /home/zzy/Genome/Red_crucian_carp.genome.fasta /home/zzy/Genome/common_carp.genome.fna delta-filter -1 -m -i 90 out.delta > out.filtered.delta show-coords -THrcld out.filtered.delta > out.filtered.coords syri -c out.filtered.coords -d out.filtered.delta -r ref.fasta -q qur.fasta

I wonder if it's because the reference genome is chromosomal and the other one is not. Thank you!

mnshgl0110 commented 10 months ago

The parameters for the show-coords command are inconsistent with the requirements for syri. Please check the readme

zzzzzzzy7 commented 7 months ago

The parameters for the show-coords command are inconsistent with the requirements for syri. Please check the readme

Thank you！