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

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pgdurand opened this Issue May 5, 2017 · 3 comments

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pgdurand commented May 5, 2017

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

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pgdurand May 5, 2017

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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.

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pgdurand commented May 5, 2017

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.

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pgdurand May 5, 2017

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PLAST v2.3 branch fixed; see commit baff670 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.

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pgdurand commented May 5, 2017

PLAST v2.3 branch fixed; see commit baff670 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.

genscale-admin pushed a commit that referenced this issue May 5, 2017

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pgdurand May 23, 2017

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fix released in v2.3.2...

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pgdurand commented May 23, 2017

fix released in v2.3.2...

@pgdurand pgdurand closed this May 23, 2017

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