Hi David,
This error message indicates some kind of inconsistency between the
sequence from which the hit was generated and the sequence which
mpiblast is either transmitting to the writer or that the writer is
attempting to write to disk. Usually this error happens when the
database isn't properly indexed, i.e. -o F has been explicitly given on
the formatdb command-line. Since the problem happens even when you
format with -o T, something else must be going wrong. One possibility
may be that a stale database fragment from a previous round of
formatting the database has somehow persisted on the compute nodes.
mpiblast performs some basic checks to identify and remove stale DB
fragments but it's possible that they may be fooled on rare occasion.
If you can, delete all uniprot* files from mpiblast local storage on
each node and from shared storage. Then reformat and run... Another
less likely possibility is that two entries in the database have
identical FastA deflines and somehow that confuses the sequence lookup
code. A --debug output and a copy of the mpiblast invocation command
line would help narrow down the problem.
-Aaron
David Lapointe wrote:
> For some reason I am having an issue with the Uniprot db. I am
> formatting it the same way as I do the ncbi dbs (nt,nr,est_*) but
> when I try to run a query I get this ( on Rocks 4.2.1).
>
> [blastall] ERROR: ncbiapi [000.000]
> gi|13661819|gb|AAK38111.1|AF360549_1: SeqPortNew:
> lcl|1634_/share/bio/ncbi/db/uniprot.035 stop(857) >= len(140)
> 4p1_11806: p4_error: interrupt SIGx: 13
> p6_32441: p4_error: interrupt SIGx: 13
> p8_14461: p4_error: interrupt SIGx: 13
> p11_30683: p4_error: interrupt SIGx: 13
> p12_30261: p4_error: interrupt SIGx: 13
> p17_8587: p4_error: interrupt SIGx: 13
> p19_32715: p4_error: interrupt SIGx: 13
> p23_31858: p4_error: interrupt SIGx: 13
> p26_785: p4_error: interrupt SIGx: 13
> ....
>
> I don't have any lines longer than 120 char.
>
> Here is the format command that I'm using (-o T with or without give
> same error).
>
> zcat uniprot.gz | mpiformatdb -i stdin -N 36 --skip-reorder -t uniprot
> -p T {-o T }
>
> David
>
>
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