Hi All,

After installing kraken am trying to build the database as specified in the manaul but getting the following messages.
Any inputs on this??

    /Tools/kraken-master/KRAKEN$ ./kraken-build --standard --threads 40 --db /home/karthic/Databases/KRAKEN
    Found jellyfish v1.1.11
    Step 1/3: performing rsync dry run...
    Rsync dry run complete, removing any non-existent files from manifest.
    Step 2/3: Performing rsync file transfer of requested files
    rsync: failed to connect to ftp.ncbi.nlm.nih.gov (165.112.9.229): Connection timed out (110)
    rsync: failed to connect to ftp.ncbi.nlm.nih.gov (2607:f220:41e:250::7): Network is unreachable (101)
    rsync error: error in socket IO (code 10) at clientserver.c(128) [Receiver=3.1.1]
    rsync_from_ncbi.pl: rsync error, exited with code 10


Thanks in Advance,
KK
Since NCBI updated their FTP website and decided to phase-out Genbank Identifiers (GIs), the default Kraken database update scripts do not work.

My colleague @Sej Modha has written a python script that helps with updating the kraken databases:
http://bioinformatics.cvr.ac.uk/blog/update-kraken-databases/