2017-10-12

BLAST+ 2.7.0 segmentation fault with HTML output

I've not managed to blog much at all this year (parenthood), so here's a quick BLAST+ bug report from working on updating the Galaxy wrappers: I've found a reproducible segmentation fault in tblastn under both Mac and Linux when requesting HTML output.


Sample FASTA data files four_human_proteins.fasta and rhodopsin_nucs.fasta are examples I use often as test cases. This example works perfectly on BLAST+ 2.6.0, here on Mac OS X

$ ~/Downloads/Software/ncbi-blast-2.6.0+/bin/tblastn -query four_human_proteins.fasta -subject rhodopsin_nucs.fasta -evalue 1e-10 -out tblastn_four_human_vs_rhodopsin.html -outfmt 0 -html -db_gencode 1 -seg no -matrix BLOSUM80

And now using the recently released BLAST+ 2.7.0, we get a segmentation fault:

$ ~/Downloads/Software/ncbi-blast-2.7.0+/bin/tblastn -query four_human_proteins.fasta -subject rhodopsin_nucs.fasta -evalue 1e-10 -out tblastn_four_human_vs_rhodopsin.html -outfmt 0 -html -db_gencode 1 -seg no -matrix BLOSUM80
Segmentation fault: 11

The same happens on Linux. In both cases I am using the pre-compiled binaries provided by the NCBI.

The critical option for triggering the crash seems to be -html to request an HTML output file, so the impact is not as bad as it could be.

I will report this bug to the NCBI by email, and update this post with any resolution.

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