I encountered an error using the script coverage_table_convert.py

[rdenise]

Description

I encountered an error using the script coverage_table_convert.py with the following command line:

coverage_table_convert.py -i comparison_binning/genomad/databases/jgi_matrix/contigs_split/jgi.ZSM103.jgi -o comparison_binning/genomad/databases/jgi_matrix/contigs_split/jgi.ZSM103.vRhyme.jgi

The error message is:

Traceback (most recent call last):
File "miniconda3/envs/vrhyme/bin/coverage_table_convert.py", line 43, in <module>
convert(args.i[0], args.o[0])
File "miniconda3/envs/vrhyme/bin/coverage_table_convert.py", line 26, in convert
sd = float(line[n+1])**0.5
IndexError: list index out of range

Steps to Reproduce

1. Run the command line provided above

Actual Behaviour

An IndexError is raised, indicating that the list line does not have the expected number of elements.

Additional Information

• Software version: vRhyme v1.1.0 (installed by conda)
• OS: Ubuntu 22.04.1 LTS

jgi.ZSM103.jgi.zip

[KrisKieft]

Hi,

Thank you for attaching the file. It looks like the JGI coverage table you have is missing the variance column, which ends in "-var". This should be standard column in jgi_summarize_bam_contig_depths --outputDepth. vRhyme assumes the input JGI coverage file has 5 total column.