Question: failed to download blast db using update_blastdb.pl + decompress db file with update_blastdb.pl
0
gravatar for arfaj a
4.5 years ago by
arfaj a10
arfaj a10 wrote:

Hello all, First, I am trying to run update_blastdb.pl script to download updated database from ncbi ftp site but, got the following error in the command prompt:

C:\inetpub\wwwroot\webclient\blast\bin>perl update_blastdb.pl refseq_rna Connected to NCBI Downloading refseq_rna (8 volumes) ... Downloading refseq_rna.00.tar.gz... Unable to close datastream at update_blastdb .pl line 181 Failed to download refseq_rna.00.tar.gz.md5!

C:\inetpub\wwwroot\webclient\blast\bin>

Any one can explain?

Second, How to decompress database file when using update_blastdb.pl? I try: perl update_blastdb.pl refseq_rna --decompress

But, got this error: Unknown option: decompress Failed to parse command line options

???

blast update_blastdb.pl ncbi • 6.2k views
ADD COMMENTlink modified 4.5 years ago by Michael Dondrup47k • written 4.5 years ago by arfaj a10

First guess: check your internet connection, try to download one of the db files using ftp or a download client in your browser:

ftp://ftp.ncbi.nlm.nih.gov/blast/db/refseq_rna.00.tar.gz.md5

99ca13b7408ea832cc110c91fd684da0  refseq_rna.00.tar.gz

ftp://ftp.ncbi.nlm.nih.gov/blast/db/refseq_rna.00.tar.gz

After you downloaded the above files, check the md5 sum manually, instructions to do this on windows are here: https://support.microsoft.com/en-us/kb/889768

Second guess: your disk is full.

ADD REPLYlink modified 4.5 years ago • written 4.5 years ago by Michael Dondrup47k

Thanks, I think it from my connection. I have another question I will post it above.

ADD REPLYlink written 4.5 years ago by arfaj a10
1
gravatar for Michael Dondrup
4.5 years ago by
Bergen, Norway
Michael Dondrup47k wrote:

Please read the documentation here, it covers all steps also for Windows users.

  • If you are having problems with the download you should try the --passive option, using passive FTP should work in most or all settings and through most or all firewall settings. If you have a personal firewall you have to allow Perl to access the internet.
  • Edit: There is no documented '--decompress' option to update_blastdb.pl, this has to be done manually afterwards unfortunately, from the documentation:

The compressed files of pre-formatted blast databases must be inflated with gzip or other decompress utilities. The working database files can then be extracted out of the resulting tar file using tar program on Unix/Linux or WinZip and StuffIt Expander on Windows and Macintosh platforms, respectively.

Edit: the decompress option is not documented in the ncbi book, but is present in the source code, since 2.2.22+ also in the latest windows version, but not in 2.2.18+ - 21! so the following should work update_blastdb.pl --decompress refseq_rna unless you have a very old version of blast, and indeed works for me, if your version is too old you should update.

ADD COMMENTlink modified 4.5 years ago • written 4.5 years ago by Michael Dondrup47k

you are right. It does not mentioned in the documentation. But, I see it in different google search like: http://devbioinfo.to.cnr.it/doku.php?id=rachaelx:blastl

ADD REPLYlink written 4.5 years ago by arfaj a10

I have checked the source code of update_blastdb and you are correct, there is an undocumented option:

"decompress"    =>  \$opt_decompress,

back to at least blast+ 2.2.22+ It uses the Archive::Tar perl module.

ADD REPLYlink modified 4.5 years ago • written 4.5 years ago by Michael Dondrup47k

Yes, I also see it in the source code on the ncbi site. The source code of my local update_blastdb.pl is different. Is it save to copy the content of update_blastdb.pl on the website to my local one? I really need to decompress.

ADD REPLYlink modified 4.5 years ago • written 4.5 years ago by arfaj a10

Update to the latest version of blast+, then perl update_blastdb.pl --decompress refseq_rna

ADD REPLYlink modified 4.5 years ago • written 4.5 years ago by Michael Dondrup47k

I actually have the latest version of blast+. It does not include the decompress in the update_blastdb.pl. Can I just replace the source code of update_blastdb.pl with the one have decompress option? is it save?

ADD REPLYlink written 4.5 years ago by arfaj a10

The latest version for windows is 2.2.31, I have checked the source and it contains the parameter. Which version do you have? I guess that you have an old script left over in the installation directory, the latest script has the following commit information:

#!/usr/bin/perl
# $Id: update_blastdb.pl 446090 2014-09-11 12:12:27Z ivanov $

You can replace the old script with the newer version, it should not depend on other blast files.

ADD REPLYlink written 4.5 years ago by Michael Dondrup47k
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