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DerrickWood / kraken2

The second version of the Kraken taxonomic sequence classification system
MIT License
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kraken2-build not progressing #663

Open talnagar opened 1 year ago

talnagar commented 1 year ago

hi We are running kraken2-build using the docker image staphb/kraken2 on about 30k genomes, we use 75 threads and 120GRAM. it's been running for 12 days and we see no progress in the logs or any files written. These are the only log msgs we see (from the first day of the run):

Creating sequence ID to taxonomy ID map (step 1)...
Sequence ID to taxonomy ID map already present, skipping map creation.
Estimating required capacity (step 2)...
Estimated hash table requirement: 61440295496 bytes
Capacity estimation complete. [35m2.270s]
Building database files (step 3)...
Taxonomy parsed and converted.
CHT created with 16 bits reserved for taxid

Is this a normal runtime? Any advice on running will be appreciated.

LiZhihua1982 commented 1 year ago

Hi would you please explain in detail how to operate? for example, first, download the genomes from NCBI in what folder? download taxonomy in what folder? Thank you very much?