peak

[ilaydagulmez]

Hi, it's me again 🥹

wgd syn completed thanks to you. Now I try thewgd peak with this command:

wgd peak 20628_8.cds.fasta.tsv.ks.tsv -ap wgd_syn/iadhore-out/anchorpoints.txt -sm wgd_syn/iadhore-out/segments.txt -le wgd_syn/iadhore-out/list_elements.txt -mp wgd_syn/iadhore-out/multiplicon_pairs.txt

I got this error:

I searched about this error but I couldn't find anything. Sorry about writing all the time...

Thanks.

[heche-psb]

Hi, could you cat wgd_syn/iadhore-out/anchorpoints.txt and show me the content? Your log showed that there were less than 2 available datapoints in analysis.

[ilaydagulmez]

Hi, sorry for my late response. Here is theanchorpoints.txt

[heche-psb]

Hi, have you tried wgd syn with your Ks data? I wonder how the anchor Ks distribution looks like.

[ilaydagulmez]

Yes, even you added the --pathiadhore parameter for my errors.

[heche-psb]

I think it's simply that your genome has sparse collinearity.

[ilaydagulmez]

Okay, I think I can't usewgd peak with syn outputs cause of my genome data.

[heche-psb]

Is scarce collinearity something you would expect? If so, it just means that your species lacks recent WGD.

[ilaydagulmez]

I'm going to research and try again the wgd peak analysis. If there is still a problem, I will reopen the issue. Thanks for your help.

[ilaydagulmez]

wgd ksd results don't show the value, is this caused of an error? I mean, I gave the ksd.tsv to syn literally and maybe it can affect the other steps. However when I tried the --pairwise parameter, the job was killed cause of 3 days limit.

Another suggest, can I BLAST my cds file before the usingwgd v2

[heche-psb]

I think I have already explained why there are Ks values as NaN.

[ilaydagulmez]

Yes, but the main question is whether the NaN values do effect the wgd syn results.

[heche-psb]

Hi, extra Ks data will lead to extra anchor Ks distribution and Ks dotplot while the original collinear results remain untouched.

[ilaydagulmez]

Thanks for your help!

[ilaydagulmez]

Hi again, I have checked my error (https://github.com/heche-psb/wgd/issues/37#issue-2331136165) and folders and I realized that my 'syn' analysis is completed, but there are no .png and .svg files, only 'i-adhore' and .tsv and .csv files. Any suggestions? Many thanks.

[heche-psb]

If there was no error log from wgd syn, I think it's because the genome has too few anchor pairs detected.

[ilaydagulmez]

Thanks for your assistance. I will attempt to filter the gene predictions. I believe there may be an issue with the number of genes I have. Thank you.

[ilaydagulmez]

Hi, even when I try with filtered cds file I get the same error:

The syn file looks like this:

I'm unsure why I can't run "peak" with "syn" files. I don't think it is caused of my genome.

[ilaydagulmez]

Hi, any suggestions? I couldn't obtain the WGD date, which is the main result file I want to get, cause of stuck in the 'syn' step. Best

İlayda