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.

Update (18 October 2017)

The BLAST team confirmed the problem on 12 October 2017, and hope to have a fix out this week - so any day now...

Update (25 October 2017)

The BLAST team have yet to release a fix, and the original BLAST+ 2.7.0 release was removed from the NCBI FTP site last week.

Update (8 November 2017)

I forgot to update this blog post at the time, but the BLAST 2.7.1 release was announced 27 October, and fixed this. I believe this issue was covered under "Fixed bl2seq problem with HTML output" in the change log.