Error in output files

[SaharSalimi]

Dear Manish,

I ran SyRI on two chromosomes from different genomes and got an error. To address an issue, I attempted to use the chrrev and fixchro scripts, but I encountered the same error when running the analysis chromosome by chromosome.

For your reference, I have attached the log file, output files, and the FASTA files used in my analysis. Additionally, I ran MCScanX on the same genomes, and it indicated that these chromosomes do not have homologous regions (synteny) together.

Could you please advise on how to resolve this error or suggest an alternative approach? I would greatly appreciate your guidance.

Thank you for your time and assistance.

SYRIv16ctxOut.txt
SYRIv16dupOut.txt
SYRIv16invOut.txt
SYRIv16invTLOut.txt
SYRIv16snps.txt
SYRIv16TLOut.txt
SYRIv16sv.txt
SYRIv16synOut.txt
SYRIv16notAligned.txt
SYRIv16invDupOut.txt
mummer_filtered_v16.delta.txt
mummer_output_v16.delta.txt
mummer_filtered_v16.coords.txt
SYRIv16syri.log.txt
slurm-453272.out.txt
chr6.fa.txt
chr1.fa.txt

Best regards,
Sahar

[mnshgl0110]

Is the uploaded mummer_filtered_v16.coords.txt file complete? It has only three alignments, as such I think the whole-genome alignment did not work and probably that is why MCScanX could not identify any homologous regions.

Please recheck the alignments. Also, make sure that for the syri run, homologous chromosomes are used. You can plot a simple dotplot to get insight into the alignments.

[SaharSalimi]

Thank you for your response.

I aimed to detect structural variations using SYRI on a chromosome-by-chromosome basis, as genomes do not consist of equal chromosomes. I wanted to make sure that SYRI cannot detect any structural variations when the chromosomes are not homologous.