[Debian-med-packaging] return code from libdivsufsort() was -1

[Fabian Klötzl]

Hi Toby,

On 24.04.2017 12:12, GURRAN Toby wrote:
> [info] Building 32-bit suffix array (length of generalized text is 0)
> Building suffix array . . . FAILURE: return code from libdivsufsort() was -1

This error message and a quick look into the libdivsufsort source code
makes me think that the true issue is within salmon: When divsufsort is
given a string of length zero, it returns -1 instead of computing the
suffix array. This seems reasonable, because the true question is, why a
client (salmon) would want a suffix array of an empty string.

> I wish to align some RNA-seq data to a Reference Transcriptome, and I am
> using the "Salmon" package to do that
> (https://github.com/COMBINE-lab/salmon). I am using Salmon version
> "*salmon*/v0.6.1-pre".
>
> Salmon makes use of a Burrows-Wheeler Transformation to index the
> reference Transcriptome, and when I run the package on my data I get
> this following error, which appears to be emanating from
> the libdivsufsort package.

My guess is that salmon doesn't like your data. Maybe it is formatted
differently than expected? I suggest contacting the salmon authors for
help. See https://combine-lab.github.io/salmon/contact/

Hope that helps,
Fabian