Chunyu Zhao

That's good news! Good luck with Sunbeam 3.0!

I recommend one of the recent ultra-fast meta-genotyping tool published in Nature Biotechnology ([github repo](https://github.com/zjshi/gt-pro)) - [GT-Pro](https://www.nature.com/articles/s41587-021-01102-3). I think it serves the goal of Sunbeam as a metagenomic sequencing pipeline...

I actually build a krakenHLL database on the cleaned eupathDB and this kmer mapping show up in my reports. Do you know why this is happening? Thanks!

@fbreitwieser this is how I built the KrakenHLL database, after downloading the [eupathDBclean files](http://ccb.jhu.edu/data/eupathDB/) and [seqid2taxid.map](http://ccb.jhu.edu/data/eupathDB/dl/seqid2taxid.map) ```bash DBNAME=testDB krakenhll-download --db $DBNAME taxonomy cp my_eupathDB_folder/*. $DBNAME/library cp seqid2taxid.map $DBNAME/library krakenhll-build --db...

I believe the output from track_markers just indicate the [progress](https://github.com/snayfach/MIDAS/blob/7ac8d6e6515b5b780132494102e4d1883fbf407b/midas/analyze/track_strains.py#L140) of sharing-alleles-compute. And I think your understanding about the actual output TSV file is correct.