Kmer-query only works with data created with bwa or bowtie2 aligner

arpcard / rgi

Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.

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Kmer-query only works with data created with bwa or bowtie2 aligner #281

Open VinzentRisch opened 2 months ago

VinzentRisch commented 2 months ago

Hello I am trying to run kmer-query on my AMR annotations and I found that I get an error when running it with a BAM file that was created with the KMA aligner in the bwt step. failed to parse BAM file: {}, please check which aligner software was used to produce the BAM file in the RGI BWT step.

Is something wrong with my BAM file or is it only possible to run kmer-query with BAM files that were created with the BWA and bowtie2 aligners?

github-actions[bot] commented 5 days ago

Issue is stale and will be closed in 7 days unless there is new activity

agmcarthur commented 4 days ago

We believe this is related to the KMA bug discussed in #256. It seems to be an edge case, i.e. does not occur for all analyses.