Hello @wwood,

I am using coverm (version coverm 0.6.1 from bioconda) to get average coverage for some metagenome assemblies to deposit to NCBI. The command I am running is coverm genome -v -m mean -t 15 --bam-files /home/projects-wrighton/NIH_Salmonella/Salmonella/Metagenomes/Megahit/LM_megahit/LM.mapped.sorted.bam -f /home/projects-wrighton/NIH_Salmonella/Salmonella/Metagenomes/Megahit/LM_megahit/final.contigs.2500.fa. When I run this error:

[2021-08-30T21:24:43Z INFO  coverm::genome] Of 18649 reference IDs, 0 were assigned to a genome and 18649 were not
[2021-08-30T21:24:43Z ERROR coverm::genome] Error: There are no found reference sequences that are a part of a genome

The mappings were generated from this reference using bbmap. To dig into this I grabbed the headers from the fasta file using grep (uploaded here: LM_headers.txt) and the headers from the bam file using idxstats (uploaded here: LM.mapped.sorted.idxstats.txt). When I look between them it looks like the headers match. Am I missing something here? Is something in the headers making the matching break?

Thanks,
Mike