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DerrickWood / kraken2

The second version of the Kraken taxonomic sequence classification system
MIT License
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Download timeout while building standard DB #679

Open jeffgauthier opened 1 year ago

jeffgauthier commented 1 year ago

While using kraken2-build --standard --use-ftp the command crashes while downloading NCBI nt data. Here is the whole output from my attempt:

Downloading nucleotide gb accession to taxon map... done. Downloading nucleotide wgs accession to taxon map... done. Downloaded accession to taxon map(s) Downloading taxonomy tree data... done. Uncompressing taxonomy data... done. Untarring taxonomy tree data... done. Step 1/2: Performing ftp file transfer of requested files Step 2/2: Assigning taxonomic IDs to sequences Processed 511 projects (925 sequences, 1.45 Gbp)... done. All files processed, cleaning up extra sequence files... done, library complete. Masking low-complexity regions of downloaded library... done. Step 1/2: Performing ftp file transfer of requested files Timeout at /cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/perl/5.30.2/lib/perl5/site_perl/5.30.2/Net/FTP.pm line 581.

This command was launched on a HPE SuperDome Flex with a download rate of about 75-100 MB/s.

LeabaeL commented 1 year ago

I had the same problem and this is the output of my attempt to download the standard database:

[localhost]$ kraken2-build --standard --threads 52 --db kraken_stddb --use-ftp
Step 1/2: Performing ftp file transfer of requested files
Step 2/2: Assigning taxonomic IDs to sequences
Processed 523 projects (943 sequences, 1.48 Gbp)... done.
All files processed, cleaning up extra sequence files... done, library complete.
Masking low-complexity regions of downloaded library... done.
Step 1/2: Performing ftp file transfer of requested files
Timeout at /home/haorui/anaconda3/envs/arg_ranker/lib/perl5/core_perl/Net/FTP.pm line 581.