Closed tpriest0 closed 2 months ago
Hello @tpriest0,
Thank you for your interest in GraphBin2.
The line where this error is coming has been commented out according to the current version of the code. Can you get the latest version of GraphBin2 from GitHub and try running again?
Let me know if the error still pops up.
Thank you!
Hey @Vini2
Thank you for the quick response.
I have cloned the git repository and recreated the conda environment.
Now I am receiving the following error:
2023-01-06 10:03:56,636 - INFO - GraphBin2 started Traceback (most recent call last): File "/XXX/XXX/XXX/software/GraphBin2/src/graphbin2_Flye.py", line 102, in
with open(contig_paths, "r") as file: FileNotFoundError: [Errno 2] No such file or directory: 'None'
This suggests a problem with the contigs file or at least the opening of it. The contigs file was produced by the 'gfa2fasta.py' script.
Many thanks
Hello @tpriest0,
Can you share with me the exact command you used to run GraphBin2?
Thank you!
Hey @Vini2
I am using the same graphbin2 command that I originally posted:
graphbin2 --assembler Flye --graph assembly_graph.gfa --contigs assembly_edges.fasta --binned metabat_contig_assignments.txt --abundance contig_depth.txt --output graphbin2_output/
Many thanks!
Hello @tpriest0,
GraphBin2 has been updated to handle the original Flye contigs. Feel free to give it a try.
Closing this issue.
Hey,
I have been trying to run Graphbin2 on a MetaFlye assembly but can't seem to get a successful run.
Steps taken: 1) Assembly with metaflye 2) Use the 'gfa2fasta.py' script to create edges fasta file 3) Map reads using minimap2 4) Determine coverage using CoverM 5) Bin contigs using metabat
From the above steps, I am trying to run GraphBin2 with the following command:
graphbin2 --assembler Flye --graph assembly_graph.gfa --contigs assembly_edges.fasta --binned metabat_contig_assignments.txt --abundance contig_depth.txt --output graphbin2_output/
However, it appears that it has a problem reading the coverage information, with the following error appearing:
Here is a snippet of the input files:
metabat_contig_assignments.txt -
contig_depth.txt -
Any idea what the solution might be?
Thanks for your time