ValueError: invalid literal for int() with base 10

[tpriest0]

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:

2023-01-05 15:38:22,105 - INFO - GraphBin2 started
Traceback (most recent call last):
File "/XXX/XXX/XXX/software/GraphBin2/src/graphbin2_Flye.py", line 115, in
coverages[contig_num] = int(strings[1])
ValueError: invalid literal for int() with base 10: '8.622175\n'

Here is a snippet of the input files:

metabat_contig_assignments.txt -

edge_491,bin_10
edge_1666,bin_10
edge_1973,bin_10
edge_2082,bin_10
edge_2827,bin_10
edge_2862,bin_10
edge_2895,bin_10
edge_3022,bin_10
edge_3110,bin_10
edge_1029,bin_11

contig_depth.txt -

edge_1 8.622175
edge_2 13.167155
edge_3 12.42515
edge_4 13.927776
edge_5 5.494654
edge_6 25.540865
edge_7 33.814053
edge_8 0
edge_9 16.802715
edge_10 4.9655805

Any idea what the solution might be?

Thanks for your time

[Vini2]

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!

[tpriest0]

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

[Vini2]

Hello @tpriest0,

Can you share with me the exact command you used to run GraphBin2?

Thank you!

[tpriest0]

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!