Assertion failed: (!gt_array_size(ss->positionmapping) || start > *(GtUword*) gt_array_get_last(ss->positionmapping)), function gt_splicedseq_add, file src/extended/splicedseq.c, line 50.

[DafniG]

Problem description

Some of my exons did not have a matching CDS. So I run the gt cds command to make sure that every exon had a CDS.

I got this message after it run for a few lines:
Assertion failed: (!gt_array_size(ss->positionmapping) || start > (GtUword) gt_array_get_last(ss->positionmapping)), function gt_splicedseq_add, file src/extended/splicedseq.c, line 50.
This is a bug, please report it at
https://github.com/genometools/genometools/issues
Please make sure you are running the latest release which can be found at
http://genometools.org/pub/
You can check your version number with gt -version.
Aborted

Exact command line call triggering the problem

gt cds -matchdescstart -seqfile hg38.fasta new.clean.gff3 > new.clean_cds.gff3

What GenomeTools version are you reporting an issue for (as output by gt -version)?

gt (GenomeTools) 1.6.1
Copyright (c) 2003-2016 G. Gremme, S. Steinbiss, S. Kurtz, and CONTRIBUTORS
Copyright (c) 2003-2016 Center for Bioinformatics, University of Hamburg
See LICENSE file or http://genometools.org/license.html for license details.

Used compiler: cc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-36)
Compile flags: -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -Wno-unknown-pragmas -O3 -Werror

Did you compile GenomeTools from source? If so, please state the make parameters used.

Yes. I run make, make test and make install

What operating system (e.g. Ubuntu, Mac OS X), OS version (e.g. 15.10, 10.11) and platform (e.g. x86_64) are you using?

My OS is CentOS 7.6.1810

[satta]

This sound like it could be a corner case depending on feature coordinates. Could you try to isolate the problematic part in your GFF and share it, together with a reference to your exact hg38.fasta please? Thanks!