Kraken - incomplete taxonomy levels/ranks in assignment

Question

[medelin.ocejo]

Hi all! In the output of Kraken, I got many assignments with uncomplete taxonomic levels like these:

d__Bacteria|p__Cyanobacteria|o__Pleurocapsales|g__Stanieria 
d__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|s__Calyptogena_okutanii_thioautotrophic_gill_symbiont

In the first case, Phylum jumps to Order and jumps to Genus. In the second, Class jumps directly to Species. So, when I try to import the abundance table to phyloseq, the taxas are not arranged correctly to its taxonomic levels. How could I fix this? I have been days browsing and could not find anything. :(

Thank you!

[h.mon]

Maybe Braken can help you.

[Sej Modha]

Have you used the scripts provided within the Kraken package to extract this info from Kraken output?

[medelin.ocejo]

Hi @Sej Modha This is the script ran:

kraken --threads 20 --db /data/db_dir/krakken_db Sample1_R1.bam Sample1_R2.bam --paired > kraken_out/Sample1.kraken
kraken-mpa-report --db /data/db_dir/krakken_db Sample1.kraken > kraken_report/Sample1.krakenReport

[Sej Modha]

I believe that Kraken works with .fasta or .fastq files? Are you sure you are getting correct results with .bam files? Kraken relies on the NCBI taxonomy data so you might want to ensure that you are using the most recent version of the Kraken and corresponding taxonomy databases.

[medelin.ocejo]

It seems that the problem is in the NCBI database. Thanks for your reply!