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Dfam-consortium / RepeatModeler

De-Novo Repeat Discovery Tool
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LtrPipeline: GenomeTools failed to run ltrharvest #202

Open panpandzf opened 1 year ago

panpandzf commented 1 year ago

image 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 commented 1 year ago

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

panpandzf commented 1 year ago

Hello, Keltonc Did you solve the problem? best

rmhubley commented 1 year ago

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 commented 1 year ago

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 "https://github.com/genometools/genometools/issues/940"

rmhubley commented 1 year ago

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