Error in creating dotplot, ValueError: cannot reindex on an axis with duplicate labels

[salmanento]

I am trying to create dotplot using two genomes for whole genome duplication detection. I am facing issue (ValueError: cannot reindex on an axis with duplicate labels) screenshot of error attached. I have also attached the Screenshot of GFF1, GFF2, Lens1 & Lens2 & Blast files used. Please look into it and guide about the issue and make me able to proceed with the analysis.

Below is the total.conf script [dotplot] blast = /home/lilin/wgd-exp/dotplot/updated/blastp_output.blast gff1 =/home/lilin/wgd-exp/dotplot/updated/X.ripnewide_gene.gff gff2 = /home/lilin/wgd-exp/dotplot/updated/S. gregaria_updatedgene.gff lens1 = /home/lilin/wgd-exp/dotplot/updated/lens1_X.riparia.lens lens2 =/home/lilin/wgd-exp/dotplot/updated/lens2_S.gregaria.lens genome1_name = Xya_riparia genome2_name = Schistocerca_gregaria multiple = 1 score = 100 evalue = 1e-5 repeat_number = 10 position = order blast_reverse = false ancestor_left = none ancestor_top = none markersize = 0.5 figsize = 10,10 savefig = /home/lilin/wgd-exp/dotplot/updated/dotplot.png

Attachments

[SunPengChuan]

There seems to be a problem when handling gff files, specifically regarding the alignment between the initial two columns in the blast file and the second column within the gff file.

[salmanento]

Thank you, resolved. Dotplot created, Please check it is Ok? Can you please help me how to interpret the dotplot results?

[SunPengChuan]

Your results show no significant collinearity between the two species. Could their divergence be too great? Consider using closer species to check if it’s a data processing issue.

[salmanento]

What about these results now?

[SunPengChuan]

The reason why the second figure doesn’t have clear synteny blocks is leading to incorrect results in your subsequent analysis.

[salmanento]

Now, I have used two closely related species, belonging from same genus. Look into the results please.