I’ve been trying to test MEGAN-LR pipeline (with LAST aligner) to classify metagenomic sample sequenced with PacBio hifi technology.
However, when trying to convert a .maf file produced by last aligner to .daa format, using maf2daa tool, i get a really small .daa file which then results in zero classified reads.
For example, with a maf file of over 500GB, i get a daa file of 17MB.
I have tried this for all three samplef for zymo gut microbiome (https://www.ncbi.nlm.nih.gov/sra/?term=pacbio%20zymo%20d6331) and also for one ATCC synthetic sample (https://www.ncbi.nlm.nih.gov/sra/SRX8173258[accn]).
To be clear, I’ve downloaded the data linked above and tested MEGAN on a subsampled portion of it. The process of subsampling was tested, and it works correctly. Some other tools (namely Kraken, we used it because it was fast), classify a significant number of reads.
Also, i have not had a similar problem with ONT zymo mock community data downloaded from Loman Labs pages (https://lomanlab.github.io/mockcommunity/).
Do you have any advice for me or can you suggest what I might be doing wrong?