contig clustering/no columns to parse error

[Leora Busse]

Hello, thank you for developing this great tool!

I've been through issues #21 and #36 where people encountered the same error as me, and used the same solutions to try to fix the issue. However, I'm still not getting the expected output. I'm using version 0.9.19 installed via bioconda. For reference, I have JAVA installed, specify the path to my ClusterONE file (I don't have the file in my $PATH, but do specify its location), and have checked the dependencies. I'm running on Mac OS, with Diamond version 0.9.21. I believe there is something wrong with the ClusterONE file, but I'm not sure how to proceed. Any recommendations? Thank you!

[Ben Bolduc]

Hi Leora,

It looks like the issue is centered around ClusterONE. A few questions:

Could you try the following:

java -version

java -jar <path-to-cluster_one-1.0.jar>

Also, what’s the first 5 or so lines for your gene-to-genome file? Does it include the headers “protein_id, contig_id, keywords” ?

-Ben

[Donna]

Hello,Ben！

I have same problem.This is my java version and gene-to-genome file.I run vcontact2 on Ubuntu.I install vcontact2 through conda.I have run it for many times,I can’t solve this problem.Would you please help me deal with it?Thank you very much!!!!

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