compare_genomes issues

assess_specific_genes.nf fails to open ORTHOGROUPS_SINGLE_GENE.NT.treefile

2

Hi, I am facing the below mention issue. I have tried to go through the module assess_specific_genes.nf and unable to resolve this on my own and would request your help....

Keevai09

Error executing process > 'PLOT'

32

Hello! I tried to run compare_genomes on several species, got an error ` Error in file(file, "r") : cannot open the connection Calls: read.nexus -> scan -> file In addition:...

StepanSaenko

RE: 4DTv and WGD

5

Hello Jefferson, My analysis includes my species of interest plus six other species. In my "comparisons_4DTv.txt", I listed single species as well as pairs of species, as follows: `` mySpecies...

Malabady

cannot open file 'ORTHOGROUPS_SINGLE_GENE.NT.timetree.nex': No such file or directory

17

Hi, I'm running compare_genomes pipeline and am having this error: Error in file(file, "r") : cannot open the connection Calls: read.nexus -> scan -> file In addition: Warning message: In...

jacquelinemattos

Can't generate venn diagram with R script

5

Hi, All the intermediate files have been created, but I'm still getting an R error to generate the venn diagram: `Attaching package: VennDiagram The following object is masked from package:ape:...

jacquelinemattos

assess_specific_genes is taking days

6

Hello, I am running the last workflow in the pipeline to assess four specific genes. My analysis included 10 plant species. the problem is that, this step is been running...

Malabady

Suitable for no model organisms?

3

Hi, I still need to go through the details. I just installed and started the Test run. We have sequenced and assembled some ciliate genomes that have never been reported....

kamalmdmostafa

Diagnosing pipeline failure

11

Hi there! Thanks again for the great tool. I've been trying it on my personal data and I think it is finishing the OrthoFinder step now. I am not sure...

jsoghigian