LtrPipeline: GenomeTools failed to run ltrharvest

[panpandzf]

my command is "repeatmodeler -pa 12 -database -database db/dbname -engine ncbi -LTRStruct &"
my system is x86_64 GNU/Linux.
the ltrharvest command in repeatmodeler is "gt ltrharvest -index esa_index -out ltrharvest.out > ltrharvest.log 2>&1".
the ltrharvest.log is empty.
my genome size is 1.2G.
my repeatmodeler version is 2.0.3 and genometools is 1.6.2
Is it a memory issue? Any help would be greatly appreciated

[Keltonc]

Encountered the same issue as yours.
My genome size is 3.3G. Memory and disk space are enough.

[panpandzf]

Hello, Keltonc
Did you solve the problem?
best

[rmhubley]

Unfortunately this is a problem with GenomeTools and something we cannot fix. Although, if you supply us with the RepeatModeler output directory from your runs, we can assist with generating a issue report for GenomeTools.

[panpandzf]

Thanks for the reply, I have solved the problem. The problem was caused by the "qsort_r.c" file in genometools. I did not use the latest "qsort_r.c" file during installation.
Refer to "genometools/genometools#940"

[rmhubley]

Thank you so much for updating this @panpandzf. I will pin this so others may benefit.