Fail to run Ltrharvest

[mscbig]

Hi, I'm running RepeatModeler on a clsuter and getting this error message:

Running LtrHarvest...sh: line 1: 13699 Aborted /usr/local/bioinfo/src/GenomeTools/genometools-1.5.10/bin//gt ltrharvest -index esa_index -out ltrharvest.out > ltrharvest.log 2>&1 LtrPipeline: GenomeTools failed to run ltrharvest. Error code: 8781824 LtrPipeline: Ltrharvest returned an unexpected result line: Assertion failed: (refrng.start <= boundaries->leftLTR_5), function gt_removeoverlapswithlowersimilarity, file src/ltr/ltrharvest_stream.c, line 1222. LtrPipeline: Ltrharvest returned an unexpected result line: This is a bug, please report it at LtrPipeline: Ltrharvest returned an unexpected result line: ... LTRPipeline: No results returned from LTR structural finder ( LtrHarvest ).

[rmhubley]

Could you list the contents of the "ltrharvest.log" file?

[mscbig]

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`.
# args=-index esa_index -out ltrharvest.out
# predictions are reported in the following way
# s(ret) e(ret) l(ret) s(lLTR) e(lLTR) l(lLTR) s(rLTR) e(rLTR) l(rLTR) sim(LTRs) seq-nr 
# where:
# s = starting position
# e = ending position
# l = length
# ret = LTR-retrotransposon
# lLTR = left LTR
# rLTR = right LTR
# sim = similarity
# seq-nr = sequence number

[rmhubley]

This is a rather late response. But for others experiencing this problem this might help. The error reported above is coming from the genometools program. If you experience this issue, you should first try to reproduce the problem by running the RepeatModeler/LTRPipeline script directly as:

LTRPipeline -threads # my_assembly.fa

Where the threads number will be the same as used with RepeatModeler. If this fails consistently, please submit the sequence file to us and the developers of the genometools software.