Indexing nt fails

[hmontenegro]

Is it possible to index NCBI nt? I tried, with fastdb -Q 0 nt nt, and after several days (10 days or so) and 399Gb database created, it segfaulted. The database files span from nt0.* to nt17.* (.bck, .des, .prj, .sds, .ssp, .suf, .tis).

[kishori82]

Usually, for such a large database we use an option for the max memory such as "-m 400000000" which is 4GB

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On Sat, Apr 22, 2017 at 12:43 AM, hmontenegro ***@***.***> wrote: Is it possible to index NCBI nt? I tried, with fastdb -Q 0 nt nt, and after several days (10 days or so) and 350Gb of database created, it segfaulted. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAj3yu1_wsnD9FX1p5igUVSShXLmlC2jks5ryYVagaJpZM4NE-Nm> .

[hmontenegro]

I got an error running with fastdb -v -m 400000000 -Q 0 nt nt:

lastdb: bad seed pattern: 400000000

Help says:

-m: seed pattern

[kishori82]

Apologies it should be -s "the volume size"

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On Sat, Apr 22, 2017 at 8:37 AM, hmontenegro ***@***.***> wrote: I got an error running with fastdb -v -m 400000000 -Q 0 nt nt: lastdb: bad seed pattern: 400000000 Help says: -m: seed pattern — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#1 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAj3ylEgjB_X87cCE_k74OMgVL0iY7z_ks5ryfSXgaJpZM4NE-Nm> .