Fails at the gplas_coocurr step
Hi Sergio,
Just trying gplas now. I'm getting an error at where i think Rscript gplas_coocurrence.R is executed. https://gist.github.com/bawee/65eee71668ec39b914f053879f97ed0c
The problem seems to be the following error?
[Thu Sep 12 16:16:36 2019]
Job 0: Creating a co-occurrence network and selecting significant associations between nodes.
Activating conda environment: /home/ubuntu/Legionella10T/projects/ecoli/starcs/anl/gplas/sw/20190912/gplas/.snakemake/conda/8b80b155
Error in 1:nrow(no_duplicated) : argument of length 0
Execution halted
[Thu Sep 12 16:17:50 2019]
The installation run worked fine with no error messages : https://gist.github.com/bawee/a6226952109d8f05d41e5f48f9773fd2
I've tried 3 different assemblies that should all contain several predicted plasmid contigs one produced with shovill and one with spades. Both give the same error. I've also tried on 2 different machines, one ubuntu14.04 and one scientific linux. Please let me know if I there are any other logs I can show you.
I've attached the graph file here. it is an E. coli contigs.gfa
Thanks,
Bryan
Edited by Bryan Wee