Error: There are no found reference sequences that are a part of a genome

[vmkhot]

Hi there!

I'm trying out coverM for the first time! I first ran the coverage "trimmed_mean" command on 18x2 read files and kept the produced bam files from mapping. It ran successfully (yay)

coverm genome -v -x fa -t 20 --methods trimmed_mean -1 ../../01_qc/qc_files/CAT_S52_R1_001.qc.fastq -2 ../../01_qc/qc_files/CAT_S52_R2_001.qc.fastq --genome-fasta-directory ../allBins/bins --bam-file-cache-directory ../../03_mapping/coverm_bam -o out_genome_coverage.tsv

Next, I wanted to use the same produced bam files to calculate relative abundances of a set of filtered genomes. I have all 18 bam files in a list in the actual command but simplified it below

coverm genome -v -x fa -t 20 --methods relative_abundance --bam-files ../../03_mapping/coverm_bam/coverm-genome.CAT_S52_R1_001.qc.fastq.bam --genome-fasta-directory ../allBins/bins/to_keep -o output_relative_abundances.tsv

However, I get the following error

I "headed" by bam file -> it looks like this

And a sample of my genome fasta files

I'm not sure but my guess is that the headers don't match? But I'm hoping for a way to make this without having to redo mapping and generate more bams again!

Any help is much appreciated!

Cheers,

Varada

[wwood]

Hey,

Yes, when you provide CoverM a set of genomes it changed the headers, because otherwise it is possible 2 contigs from different genomes have the same name, which confuses things.

If you want to re-use the BAM files I suggest using -s '~' instead of genome-fasta-directory.

HTH

[vmkhot]

ok, that seems to have worked!

Thanks again

V