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Dotplots.svg and ks_anchors.tsv files are empty #78
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Hi Muthulakshmi, I downloaded the enclosed file "sample.tar.gz" from you and reran the collinearity analysis successfully. Here is my step: First, I reformat the gene ID of the CDS file "sample.fasta" to make it match the GFF file "ath.gff" in a python session:
Now I got the reformatted CDS file "sample.fa.cds" for next step; To infer paralogous gene family, I used command:
##Note that there were quite some genes that couldn't be correctly translated. And I got two files in the "wgd_dmd" directory, "sample.fa.cds.mcl" and "sample.fa.cds_sample.fa.cds.tsv"; Next I inferred the collinearity based on the freshly-gained gene family information (assumed that I was still in the same directory which contained the original data):
The resulting file "sample.fa.cds.mcl.dotplot.svg" in directory "wgd_syn" is the inferred intraspecific collinear dotplot, as shown below. Given the successful run of "wgd syn" without Ks data, I suppose it will also be no problem for another run with Ks data. It's weird that your result file "sample.fasta.blast.tsv.mcl.dotplot" was even empty. Do you have the log file of that failed run, we can diagnose further in detail based on that log. |
sample.tar.gz |
Hi, I have the same problem while running wgd syn .The .tsv file and .mcl file seem to be right, but the Dotplots.svg and ks_anchors.tsv files are empty. There are not error report in log file. I get the same problem while using sample.fa, ath.fa and my own data. This is the result of sample.fa after running wgd syn , could you please help me to sort out. |
Meanwhile, I run the code above as |
Could you please provide the version of wgd you were using? And the version of other python packages. Thanks. |
(wgd) [zhaoli@mn02 example]$ conda list |
Hi, there is no multiplicon found in your run. I guess there might be a gene id extraction issue. Could you make sure that you give correct feature and attribute as in gff3 and family files?
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I think you might need to check whether there is any multiplicons found in the first place. The log provided by @muthu1722 shows no multiplicons found by
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Hi, I have used supplementary material to run WGD. I am able to rum till wgd syn without any issue but in the wgd_syn results only dotplot as well as ks_ancjors.tsv files are empty. I have also tried with one sample data just to confirm whether the data am using creating any trouble but again with sample data I have got the same issue but other than these two files my histogram, tsv.mcl files are looking fine for both sample data and my own data. I am attaching my sample data as well as output for your refernce. It would be really helpful if you could help me to resolve it .
Thank you in advance.
Muthulakshmi
sample.tar.gz
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