PLAST fails to create XML file using NCBI nr databank

PLAST-software / plast-library

PLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations.

http://plast.inria.fr

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PLAST fails to create XML file using NCBI nr databank #1

Closed pgdurand closed 7 years ago

pgdurand commented 7 years ago

while running Plastp against a recent release of NCBI nr databank, the software finishes with a segmentation fault.

Cmd-line is as follows: plast \ -p plastp \ -d /db/nr/blastDB/nr.pal \ -i test.fa \ -o test.fa.nr.plastp.xml \ -e 5e-5 -a 8 -max-hsp-per-hit 1 -max-hit-per-query 10 \ -seeds-use-ratio 100 \ -outfmt 4 \ -force-query-order 1000 \ -bargraph

pgdurand commented 7 years ago

Tests:

Plast v2.3 branch on OSX: OK
Plast v2.3 branch on Linux: KO

Identified problem was: when running Plast against 'nr.pal' alias, Plast uses the entire list of all 62 blastdb volumes which appears to be a far-too-long string (2188 chars) to write as the BlastOutput_db element of the XML result: this is the reason why we got an out-of-array exception.

pgdurand commented 7 years ago

PLAST v2.3 branch fixed; see commit baff6706f on branch v2.3. New release 2.3.2 to come by May, 11th. This issue will be closed as soon as PLAST patch is released.

pgdurand commented 7 years ago

fix released in v2.3.2...