Running flye assemblies and getting error wanting contigs.paths file for spades

Open emilyjunkins opened this issue 1 year ago • 0 comments

Hello,

I am running graphbin v 1.7.1 and python version 3.10.13

First, I was unable to get the python support scripts to work so I renamed all of my files to make naming consistent and made the csv file with custom scripts.

When I tried to run the following code:

graphbin --contigs /home/ejunkins/LS01_hifi_coveragebin/LS01_001_assembly_renamed_edges.fasta --binned /home/ejunkins/LS01_hifi_coveragebin/bins/001/contignames/edges/LS01_001_all_edges_graphbin.csv --graph /home/ejunkins/jgi_assemblygraphs/NGXTG/flye/assembly_graph.gfa --output /home/ejunkins/LS01_hifi_coveragebin/bins/001/graphbin_out --prefix graphbin_metabat2_LS01_001_bin_with_cov --assembler flye

I get this error: 2024-02-12 12:28:23,452 - ERROR - Please make sure to provide the path to the contigs.paths file. 2024-02-12 12:28:23,453 - INFO - Exiting GraphBin... Bye...!

My understanding was that this was only for spades assemblies...

Feb 12 '24 20:02 emilyjunkins