I have an approximately 40 kb size assembly of a portion of a bacterial genome. When I run it on Kraken2 it comes out as unclassified but when I take the same sequence and run it through Blastn I get a match to a known organism. I have checked and the specific species is in my krakendb. I also ran the full genome of the same species, different strain and was to classify the organism correctly.
./kraken2 \
--db /kraken2-2.1.3/KRAKEN2_DIR/kraken2db \
--threads 8 \
--classified-out /kraken2-2.1.3/KRAKEN2_DIR/kraken2db/reports/classified_36 \
--report /kraken2-2.1.3/KRAKEN2_DIR/kraken2db/reports/new36.k2report \
--report-minimizer-data /kraken2-2.1.3/KRAKEN2_DIR/kraken2db/reports/new36mini.k2report \
--minimum-hit-groups 2 \
--confidence 0.5 \
/36_final_nobb.fasta
I have an approximately 40 kb size assembly of a portion of a bacterial genome. When I run it on Kraken2 it comes out as unclassified but when I take the same sequence and run it through Blastn I get a match to a known organism. I have checked and the specific species is in my krakendb. I also ran the full genome of the same species, different strain and was to classify the organism correctly. ./kraken2 \ --db /kraken2-2.1.3/KRAKEN2_DIR/kraken2db \ --threads 8 \ --classified-out /kraken2-2.1.3/KRAKEN2_DIR/kraken2db/reports/classified_36 \ --report /kraken2-2.1.3/KRAKEN2_DIR/kraken2db/reports/new36.k2report \ --report-minimizer-data /kraken2-2.1.3/KRAKEN2_DIR/kraken2db/reports/new36mini.k2report \ --minimum-hit-groups 2 \ --confidence 0.5 \ /36_final_nobb.fasta
1 sequences (0.04 Mbp) processed in 0.014s (4.4 Kseq/m, 182.13 Mbp/m). 0 sequences classified (0.00%) 1 sequences unclassified (100.00%)