gt ltrclustering

[ohan-Bioinfo]

Problem description

after the identification of LTR through Ltrharvest and annotation using Ltrdigest , I'm facing an error while trying to use (ltrsift) ltrclustering to group the output into families

Exact command line call triggering the problem

gt ltrclustering -psmall 80 -plarge 30 -o Out_clustring_ltrdigest index.fna Ltrdigst.gff

##Error output

gt ltrclustering -psmall 80 -plarge 30 -o Out_Clustrer index.fna Ltrdigst_Result.gff 
Assertion failed: (eb->plainseq), function gt_encseq_builder_build, file src/core/encseq.c, line 9098.
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`.
Abort trap: 6

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

gt (GenomeTools) 1.5.10
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: Apple LLVM version 10.0.0 (clang-1000.11.45.2)
Compile flags:  -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -Wno-unknown-pragmas -O3 -m64 -Qunused-arguments -Wno-parentheses -Werror

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

yes

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?

Mac OS Mojave version 10.14

[satta]

Thanks for reporting this! Can you please provide an example input set (sequence/index and GFF) for us to reproduce the problem?

[satta]

Thanks, but I'm afraid I will need both complete input files. The sequence provided by you above looks a bit short (and in a strange format) and the GFF consists of only one element with coordinates that do not seem to match the sequence length.

[ohan-Bioinfo]

I just take a part of the sequences and shared it here. should I share all of it here (copy&past) or its possible to attach it here @satta for the gff part as you said i copied only one element
the data is big

[satta]

If that's OK with you, you could use a file hosting service such as Dropbox etc. to provide the files or drag & drop them into the comment box to upload them here.. Please avoid pasting long content here.

[satta]

Yes, it seems to work. I will need some time to look into the issue though...