Error with Formatdb of legacy blast?

Question

[DanielC]

Dear Friends,

When running formatdb like this:

blast/bin/formatdb -o T -i nr_pfilt
[formatdb] ERROR: Using 1000000000 bases per volume will exceed the maximum number
of volumes formatdb can create.
Please increase this value or do not set it at all.

I get the above error, can you please let me know how can I resolve this issue?

Thanks!

Answer 1

[Mensur Dlakic]

It may fix it if you use a larger value with -v switch. It seems that with your version it is set to 1000, though mine has -v 4000. To see what the options and defaults are, type blast/bin/formatdb -. You may also want to set -p T.

[DanielC]

Thanks! I did as you suggested and increased the value like this:

formatdb -o T -i nr_pfilt -v 160000000000 -p T
[formatdb] FATAL ERROR: Volume size may not exceed 16 gigabases.

And, when I do:

formatdb -o T -i nr_pfilt -v 16000000000 -p T
[formatdb] ERROR: Using 1000000000 bases per volume will exceed the maximum number
of volumes formatdb can create.
Please increase this value or do not set it at all.

Could you please give your suggestions on what could be the problem here? Thanks

[Mensur Dlakic]

Depending on your version of formatdb, the -v switch refers to millions of bases. So your command is asking for too many bases. Like I said, type formatdb - and see if that helps you with its version and the command switch format.

[DanielC]

IT works now:

formatdb -o T -i nr_pfilt -v 10000

Thanks!