Problem Downloading The Nt Database From Ncbi
2
2
Entering edit mode
10.4 years ago
Anjan ▴ 830

I am using the NCBI script update_blastdb.pl script thus:

 update_blastdb.pl --verbose --force nt.
I get the following message:
Net::FTP>>> Net::FTP(2.77)
Net::FTP>>>   Exporter(5.58)
Net::FTP>>>   Net::Cmd(2.29)
Net::FTP>>>   IO::Socket::INET(1.29)
Net::FTP>>>     IO::Socket(1.29)
Net::FTP>>>       IO::Handle(1.25)
Net::FTP=GLOB(0x8df5a8)<<< 220-
Net::FTP=GLOB(0x8df5a8)<<<  Warning Notice!
Net::FTP=GLOB(0x8df5a8)<<<  
Net::FTP=GLOB(0x8df5a8)<<<  This is a U.S. Government computer system, which may be accessed and used
Net::FTP=GLOB(0x8df5a8)<<<  only for authorized Government business by authorized personnel.
Net::FTP=GLOB(0x8df5a8)<<<  Unauthorized access or use of this computer system may subject violators to
Net::FTP=GLOB(0x8df5a8)<<<  criminal, civil, and/or administrative action.
Net::FTP=GLOB(0x8df5a8)<<<  
Net::FTP=GLOB(0x8df5a8)<<<  All information on this computer system may be intercepted, recorded, read,
Net::FTP=GLOB(0x8df5a8)<<<  copied, and disclosed by and to authorized personnel for official purposes,
Net::FTP=GLOB(0x8df5a8)<<<  including criminal investigations. Such information includes sensitive data
Net::FTP=GLOB(0x8df5a8)<<<  encrypted to comply with confidentiality and privacy requirements. Access
Net::FTP=GLOB(0x8df5a8)<<<  or use of this computer system by any person, whether authorized or
Net::FTP=GLOB(0x8df5a8)<<<  unauthorized, constitutes consent to these terms. There is no right of
Net::FTP=GLOB(0x8df5a8)<<<  privacy in this system.
Net::FTP=GLOB(0x8df5a8)<<<  ---
Net::FTP=GLOB(0x8df5a8)<<<  Welcome to the NCBI ftp server! The official anonymous access URL is ftp://ftp.ncbi.nih.gov
Net::FTP=GLOB(0x8df5a8)<<<  
Net::FTP=GLOB(0x8df5a8)<<<  Public data may be downloaded by logging in as "anonymous" using your E-mail address as a password.
Net::FTP=GLOB(0x8df5a8)<<<  
Net::FTP=GLOB(0x8df5a8)<<<  Please see ftp://ftp.ncbi.nih.gov/README.ftp for hints on large file transfers
Net::FTP=GLOB(0x8df5a8)<<< 220 FTP Server ready.
Net::FTP=GLOB(0x8df5a8)>>> USER anonymous
Net::FTP=GLOB(0x8df5a8)<<< 331 Anonymous login ok, send your complete email address as your password.
Net::FTP=GLOB(0x8df5a8)>>> PASS ....
Net::FTP=GLOB(0x8df5a8)<<< 230 Anonymous access granted, restrictions apply.
Net::FTP=GLOB(0x8df5a8)>>> CWD /blast/db
Net::FTP=GLOB(0x8df5a8)<<< 250 CWD command successful
Net::FTP=GLOB(0x8df5a8)>>> TYPE I
Net::FTP=GLOB(0x8df5a8)<<< 200 Type set to I
Connected to NCBI
Net::FTP=GLOB(0x8df5a8)>>> PORT 10,0,1,2,192,59
Net::FTP=GLOB(0x8df5a8)<<< 500 Illegal PORT command
nt not found, skipping.
Net::FTP=GLOB(0x8df5a8)>>> QUIT
Net::FTP=GLOB(0x8df5a8)<<< 221 Goodbye.

The script has worked in the past. Is anyone having similar problems? Any suggested trouble-shooting steps would be appreciated. Thanks, Anjan

ncbi download scripting perl • 4.2k views
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4
Entering edit mode
10.4 years ago

You need to enable Passive Transfers

Net::FTP class has a method that you can use:

pasv ()

    Tell the server to go into passive mode.
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0
Entering edit mode
4.1 years ago
Carlos Borroto ★ 2.0k

In case someone finds this thread while searching for this issue, you can ask update_blastdb to use passive mode.

$ update_blastdb --passive --decompress nt
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