Blastdbcheck Error
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11.1 years ago
Matt ▴ 60

I keep getting errors on the following command:

blastdbcheck -db nt.00
Writing messages to <stdout> at verbosity (Summary)
ISAM testing is ENABLED.
Legacy testing is DISABLED.
By default, testing 200 randomly sampled OIDs.

Testing 1 volume(s).
  /home/envdev/data/blast/db/nt.00 / MetaData:   [ERROR] caught exception.
 Result=FAILURE. 1 errors reported in 1 volume(s).
Testing 0 alias(es).
 Result=SUCCESS. No errors reported for 0 alias(es).

Total errors: 1

I downloaded via the update script, checked the md5 checksum, and unzipped the file.

Anyone seen this?

The box has 48 GB of memory.

Thanks!

Matt

blast ncbi • 5.0k views
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blastdbcheck -db 16SMicrobial

the same error

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11.1 years ago
Digiomics ▴ 170

I have never used the blastdbcheck command before, but I just tried it with all my blast databases (some from the NCBI, some custom made) and different tests (random, ends) and got the same error message. So it seems to be a general problem with blastdbcheck.

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Good to know. Thank you!

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I agree, I just tested with the native ncbi nr blastdb ang got the same error

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Still getting this error when running blastdbcheck on the native NCBI nt database, over a year later. This page is currently the top google result for "blastdbcmd"

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Are you doing

blastdbcheck -db nt.00

or

blastdbcheck -db nt

The first isn't a database whereas the second is..

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4.6 years ago
Leonardo ▴ 30

Years after but error still persists. In the following link you can find a solution provided by user "carlosproca", which just worked for me. It is something related to taxon id files.

http://seqanswers.com/forums/archive/index.php/t-34826.html

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