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How much time should be expected for building a database by kraken2-build? #149

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Minh2021 opened this issue Jan 27, 2021 · 0 comments
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@Minh2021
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Hello,

I am trying to build a database containing non-redundant nucleotide sequences from NCBI (NCBI_nt) and some other rumen genomes downloaded from the other website. Following Kraken2's manual, I could download NCBI taxonomy, NCBI_nt database and add the rumen genomes into the database. These steps were successfully done. However, when processing step 3 which is building the database, although there has been no error message, it has been running for a long time (43 hours). I checked the server and saw that the program is still running; however, I did not see any new output in the last 24 hours. My question is how long should I expect to wait for the process to be finished? Does it usually take this long time?

Followings was the command line I used and what appeared on my screen:

./kraken2-build --build --threads 20 --db $DBNAME
Creating sequence ID to taxonomy ID map (step 1)...
Found 72450193/72530381 targets, searched through 779285158 accession IDs, search complete.
lookup_accession_numbers: 80188/72530381 accession numbers remain unmapped, see unmapped.txt in DB directory
Sequence ID to taxonomy ID map complete. [20m26.938s]
Estimating required capacity (step 2)...
Estimated hash table requirement: 219511709988 bytes
Capacity estimation complete. [58m59.084s]
Building database files (step 3)...
Taxonomy parsed and converted.
CHT created with 22 bits reserved for taxid.
Processed 13414311 sequences (68169888726 bp)...

Any information from you will be much appreciated. Thank you so much!

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