--checkm-tab-table

[sarehaghababaee]

I am using CoverM version 0.7.0.
I ran the following command to calculate relative abundance, mean coverage, and to perform genome clustering and dereplication, but I encountered the following error:
Command:
cpmmand: coverm genome
-1 "$dir/04.trimmed_fasta/${SAMPLE}_1.fa"
-2 "$dir/04.trimmed_fasta/${SAMPLE}_2.fa"
--genome-fasta-directory "$dir/25.CoverM/genomes"
-x fa
--output-file "$dir/25.CoverM/coverm_output/${SAMPLE}_coverm.tsv"
--output-format dense
--methods relative_abundance mean
--min-read-percent-identity 95
--min-read-aligned-percent 75
--dereplicate
--checkm2-quality-report "$dir/17.checkm2/output/quality_report.tsv"
--min-completeness 0
--max-contamination 100
--dereplication-quality-formula completeness-5contamination
--dereplication-output-cluster-definition "$dir/25.CoverM/coverm_output/cluster_definitions.tsv"
--dereplication-output-representative-list "$dir/25.CoverM/coverm_output/representative_paths.txt"
--threads "$THR"
Error:
the following required arguments were not provided: --checkm-tab-table
I only ran CheckM2 and have the quality_report.tsv output from it. I did not run the original CheckM. What should I do in this case?
In another attempt, I added the --checkm-tab-table argument and gave it the same quality_report.tsv from CheckM2. The command I ran was:
Commnad:
coverm genome
-1 "$dir/04.trimmed_fasta/${SAMPLE}_1.fa"
-2 "$dir/04.trimmed_fasta/${SAMPLE}_2.fa"
--genome-fasta-directory "$dir/25.CoverM/genomes"
-x fa
--output-file "$dir/25.CoverM/coverm_output/${SAMPLE}_coverm.tsv"
--output-format dense
--methods relative_abundance mean
--min-read-percent-identity 95
--min-read-aligned-percent 75
--dereplicate
--checkm2-quality-report "$dir/17.checkm2/output/quality_report.tsv"
--checkm-tab-table "$dir/17.checkm2/output/quality_report.tsv"
--min-completeness 0
--max-contamination 100
--dereplication-quality-formula completeness-5contamination
--dereplication-output-cluster-definition "$dir/25.CoverM/coverm_output/cluster_definitions.tsv"
--dereplication-output-representative-list "$dir/25.CoverM/coverm_output/representative_paths.txt"
--threads "$THR"

conda deactivate
echo "Done: $(date)."
However, I received the following error:
error parsing contamination in checkm tab table: ParseFloatError { kind: Invalid }
Could you guide me how can I solve this issue?

[wwood]

Hi,

Looks like something is amiss with your input table - what is the format?

[sarehaghababaee]

The input table is in tsv format. Exactly the output of CheckM2.

[wwood]

OK. If it is CheckM2 you should use --checkm2-quality-report instead. tab-table is for checkm1.

[sarehaghababaee]

As I explained above, in my first attempt I used --checkm2-quality-report and used the output of CheckM2 as the input for this command. But, I faced the error that I need to provide --checkm-tab-table as well.

[wwood]

Oh you are quite right - my mistake in reading too quickly. This is a straight up bug - when you specify --min-completeness/max-contamination it requires checkm-tab-table, and that requirement was never updated when checkm2 support was added. I've now fixed that in the main branch, and it'll be fixed in the next release.

In the meantime I think it might be possible to use coverm cluster, and then coverm genome on the clustered outputs?

Or just using the main branch.

Thanks for the report. ben

[sarehaghababaee]

Thanks for your response.
Just to clarify, I ran Coverm genome directly on the full set of genomes, without clustering them first. Are you suggesting that I should first run Coverm cluster and then use the clustered outputs as input for Coverm genome?

[wwood]

When you "ran Coverm" do you mean with the above command? If so it has --dereplicate so that is cluster and then map, all in one command.

If you did not cluster first, then you'll probably want to - otherwise reads get multi-mapped between closely related species, and that throws off abundance calculations.

HTH

[wwood]

Are you suggesting that I should first run Coverm cluster and then use the clustered outputs as input for Coverm genome?

Yes, exactly