Downloading blastdb nr database can't --decompress

[kuheng3]

Hi,
I have tried to download nr database using "update_blastdb.pl nr --decompress". Downloading the database is fine but when it start decompressing files. I keep getting:

kuheng@Ku ~/blast/db/nr
$ update_blastdb.pl nr --decompress
Connected to NCBI
Downloading nr (55 volumes) ...
Decompressing nr.00.tar.gz ...Read error on tarfile (missing data) 'nr.pdb' at offset unknown at /Users/kuheng/miniconda3/envs/bioinfo/bin/update_blastdb.pl line 496.
Invalid header block at offset unknown at /Users/kuheng/miniconda3/envs/bioinfo/bin/update_blastdb.pl line 496.
Invalid header block at offset unknown at /Users/kuheng/miniconda3/envs/bioinfo/bin/update_blastdb.pl line 496.
Invalid header block at offset unknown at /Users/kuheng/miniconda3/envs/bioinfo/bin/update_blastdb.pl line 496.
Is there any solution to fix the update_blastdb.pl?
Thank you

[ialbert]

Can you try adding an additional parameter:

--source ncbi 

the source should be automatically detected but sometimes it is not set properly

[kuheng3]

Hi Dr. Ialbert,
I tried update_blastdb.pl nr --source ncbi --decompress. Here is the result I got:
kuheng@Ku ~/blast/db/nr
$ update_blastdb.pl nr --source ncbi --decompress
Connected to NCBI
Downloading nr (55 volumes) ...
Decompressing nr.00.tar.gz ...Read error on tarfile (missing data) 'nr.pdb' at offset unknown at /Users/kuheng/miniconda3/envs/bioinfo/bin/update_blastdb.pl line 496.
Invalid header block at offset unknown at /Users/kuheng/miniconda3/envs/bioinfo/bin/update_blastdb.pl line 496.

[ialbert]

I have now tried it myself, indeed it raises an error for me as well.

Goes to show that not even NCBI is capable of publishing data/tools as simple as one that just downloads data. What hope is there for regular scientists?

A possible workaround is to manually decompress the file that is already there:

tar zxvf nr.00.tar.gz 

then reissue the original command again,

update_blastdb.pl nr --source ncbi --decompress

it should continue on with downloading and decompressing the next file, I did not check if those work or not.

For a deeper understanding of what is going on, the tool automates the downloads from this location:

https://ftp.ncbi.nlm.nih.gov/blast/db/

to do the same from command line you would do:

wget https://ftp.ncbi.nlm.nih.gov/blast/db/nr.00.tar.gz

followed by:

 tar zxvf nr.00.tar.gz 

If the original command does not work, now you need to automate that for all 54 files :-/

[kuheng3]

Hi Dr. Ialbert,
Thank you so much, I will try the methods you mentioned. I wasn't sure if is my computer setting issue or the perl script. If the "tar zxvf nr.00.tar.gz" + "update_blastdb.pl nr --source ncbi --decompress" didn't work. I will use a script to unzip all nr.tar.gz files.