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DerrickWood / kraken2

The second version of the Kraken taxonomic sequence classification system
MIT License
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does not contain necessary file taxo.k2d #552

Open ramnageena11 opened 2 years ago

ramnageena11 commented 2 years ago

Hi, I have installed the Kraken database but same error is coming again and again. that taxo.k2d is missing while file can be seen after installation. But there are no folders after uncompressing/installation.

(base) powersequencing@CH-CB-RS-P5820:~$ tar -xzvf /media/powersequencing/10TB-STORAGE/ram/kraken2_db/16S_Silva138_20200326.tgz 16S_SILVA138_k2db/ 16S_SILVA138_k2db/database250mers.kmer_distrib 16S_SILVA138_k2db/database75mers.kmer_distrib 16S_SILVA138_k2db/opts.k2d 16S_SILVA138_k2db/README.md 16S_SILVA138_k2db/database100mers.kmer_distrib 16S_SILVA138_k2db/taxo.k2d 16S_SILVA138_k2db/hash.k2d 16S_SILVA138_k2db/database150mers.kmer_distrib 16S_SILVA138_k2db/database50mers.kmer_distrib 16S_SILVA138_k2db/database200mers.kmer_distrib (base) powersequencing@CH-CB-RS-P5820:~$ kraken2 --db /media/powersequencing/10TB-STORAGE/ram/kraken2_db/16S_SILVA138_k2db /media/powersequencing/10TB-STORAGE/ram/metagenome_data/Ram-Metag-07-14-21/full_run/allreads_combined/medaka_final2/rRNAs_medaka_final_2.fasta --output /media/powersequencing/10TB-STORAGE/ram/metagenome_data/Ram-Metag-07-14-21/full_run/allreads_combined/medaka_final2/results_kraken_rRNAs_medaka_final_2 --unclassified-out unclassified_16S --classified-out classified_16S --threads 20 kraken2: database ("/media/powersequencing/10TB-STORAGE/ram/kraken2_db/16S_SILVA138_k2db") does not contain necessary file taxo.k2d

jenniferlu717 commented 2 years ago

I'm not 100% if this will fix your issue but can you rerun the kraken2 command line and move the sequence file to the end of the line?

NazifaMoumi commented 2 years ago

Hi, have you found any solution to this problem? I'm facing the same issue.

_./kraken2-build --standard -db BUILTDB2 --threads 64 --no-masking

./kraken2 -db BUILTDB --threads 64 --paired [read1] [read2]_

I'm using the above commands. The database building command runs smoothly but the classifying command gives the error it does not contain the necessary file taxo.k2d.

russellsmithies commented 1 year ago

Not sure if anyone has found a solution, but I discovered that I get this error if there are symlinks in the database path. If I use the full path then it works OK.