Assertion failed: (idx < gt_encseq_num_of_sequences(bs->encseq) && end >= start)

[HengyouZhang]

Problem description

I am using genome threader to train a non-model plant species download from Phytozome for Bssm file. After I got the gff3 file with gth as described in the manual (threader manual, section 9, page 32), I used gthbssemtrain to train the file, but get the following error related to genome tools. Please help me out, thanks.

Exact command line call triggering the problem

$ /Applications/gth-1.7.1-Linux_x86_64-64bit/bin/gthbssmtrain -seqfile Esalsugineum_173_v1.fa -outdir esa.bssm.train -force Esa.gth.gff3
gt-ag:  87.94% (n=166593)
gc-ag:   1.75% (n=3315)
Assertion failed: (idx < gt_encseq_num_of_sequences(bs->encseq) && end >= start), function gt_bioseq_get_sequence_range, file src/core/bioseq.c, line 388.
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 (core dumped)
$ /Applications/gth-1.7.1-Linux_x86_64-64bit/bin/gth -version
gth (GenomeThreader) 1.7.1

Example minimal input triggering the problem

don't know

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

genometools-1.5.9

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

yes, make used

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?

Red Hat Linux, x86_64

[longzhangnation]

I was wondering whether you have solved the problem because I met the same situation, so how did you solve it ?

[longzhangnation]

maybe the gff3 file is wrong ,you can try to find which line is wrong by testing part of your file .the delete that line .