David Emms

It'd be great to see it working on the tutorial data, Ensembl is widely used and I'd love to get to try it on some of my analyses!

Are you using the latest version of OrthoFinder? If not then try updating and check if the issue has already been fixed.

You can restart from the trees using the "-ft" option.

Hi @shiyi-pan In the message it also says that it is tryign to run this search command, does it work if you run it outside OrthoFinder? ``` /gss1/home/hjb20181119/panyongpeng/NN1138-2/03.orthofinder_data/02.SoybeanData/diamond/diamond blastp -ignore-warnings...

Hi If you use the option "-M msa" then it will infer a species tree with a concatenated multiple sequence alignment of single-copy genes. These are genes which are single...

Hi Sowptika If n>1000 then that if fine, it means it has lots of data. You say the tree could not be constructed, do you have information that suggests it...

Good suggestion, I'll put it on the list and try and get it done soon. All the best David

Is raxml still running? RAxML will take a very long time to infer the first 1000 trees. Have you tried running the line `top` command to see what process are...

Hi Hu ShaSha Would you be able to send me a link that I can download your input files from and I will try and debug the issue. The address...

Just the protein sequence files. You'll need to send a link, replying to github with an email attachment doesn't work.