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Problems with downloading the standard database #551

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SergeyBaikal opened this issue Jan 15, 2022 · 0 comments
Open

Problems with downloading the standard database #551

SergeyBaikal opened this issue Jan 15, 2022 · 0 comments
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download issue kraken2-build --download-library issue

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@SergeyBaikal
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SergeyBaikal commented Jan 15, 2022

  1. I see that the problem has not been solved with downloading the databases, partly because of the NСBI.
    I have a problem even when specifying --use-ftp. I'm from Russia and after downloading about 1.5 GB, the connection is broken. And the download speed is very, very slow. I tried to download both from my home computer and from my work.
    kraken2-build --standard --threads 4 --use-ftp --db /media/sf_Shared_Folder/
    After several attempts, I get an empty command prompt after typing this command and nothing happens.

  2. Through rsync change FTP to HTTPS
    rsync_from_ncbi.pl: unexpected FTP path (new server?) for na PapenfussLab/gridss#540 (comment)

  3. Use only the home directory, otherwise there will be permission issues.

  4. Who has a proxy at work, write this in the bashrc file: export RSYNC_PROXY="proxy:port"
    proxy and port your organization, for example 127.0.0.1:3128

  5. I saw an amazing thing. Download progress is not shown, even the file does not appear in the folder. It appears after download.
    The database -standard already occupies more than 170 GB!

  6. If you have problems downloading the plasmid database, then change the script.
    Use HTTPS instead for plasmids, update path #529 (comment)

  7. In order not to start installing all the databases, install those that could not be installed.
    kraken2-build --download-library plasmid --db kraken-Sdb
    kraken2-build --build --db kraken-Sdb --threads 32

It turns out that there is already an assembled database ...
https://benlangmead.github.io/aws-indexes/k2

@jenniferlu717 jenniferlu717 added the download issue kraken2-build --download-library issue label Mar 14, 2022
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