Error. No file(s) for coverage information were identified. Check coverage inputs (c/b/s/r/u/v). Exiting.

[haleyhallowell]

Hello!

Super pumped to try out vRhyme. I followed instructions in downloading/installing from source and using pip to a conda environment. test_vRhyme.py as well as a test run with example data worked perfectly. However, when i use my own data with the following code :
vRhyme -i all_vOTUs_combined_virome.fna -b bam_files/*.bam

I get this error:

/home/hhallow1/.conda/envs/vRhyme/bin/vRhyme:16: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
  import pkg_resources

Error. No file(s) for coverage information were identified. Check coverage inputs (c/b/s/r/u/v). Exiting

I'm confused because i am specifying .bam files, which seems like should be enough to calculate coverage. Any ideas of fixing this? Thanks!

[cody-mar10]

Hi Haley,

Are you still experiencing this issue? If so, could you show what your package versions are for all the tools in your vRhyme environment?

Cody

[KrisKieft]

It may be possible that no reads within any bam files specified had any alignments to the sequences input. The error message is actually a little misleading. This error can pop up after the bam files have been converted into the coverage table. Check "vRhyme_coverage_files/vRhyme_coverage_values.tsv" and make sure it's not empty.

[metapanpanwang]

hi, I have the same problem. i use my own data with the following code :
vRhyme -i fasta -g genes -p proteins -r paired_reads_folder/*.fastq -t threads -o output_folder --method longest
I get this error:
Error. No file(s) for coverage information were identified. Check coverage inputs (c/b/s/r/u/v). Exiting.