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Dfam-consortium / RepeatModeler

De-Novo Repeat Discovery Tool
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Broken symbolic link on error in LTR_Retriever #240

Closed benfulton closed 3 months ago

benfulton commented 6 months ago

Describe the issue

A symbolic link is created for LTR_Retriever from tmpInputSeq to seq.fa in the temporary directory. If LTR_Retriever fails, tmpInputSeq is deleted but the link remains. This makes reproducing the LTR error difficult.

Reproduction steps

  1. Break LTR_Retriever in some way (remove a dependency perhaps)
  2. RepeatModeler -database test -threads 1 -LTRStruct

Log output 

LTRPipeline::runLtrRetriever : Running analysis cd /N/scratch/befulton/repeatmodeler_test/RM_108867.MonMar251020042024/LTR_114100.MonMar251026312024/LRET_114100.MonMar251026402024; /N/soft/rhel8/repeatmodeler/ltr_retriever/2.9.0/LTR_retriever  -repeatmasker /N/soft/rhel8/repeatmasker/4.1.5 -blastplus /N/soft/rhel8/repeatmasker/rmblastn/2.13.0/bin -cdhit_path /N/soft/rhel8/repeatmodeler/cdhit/4.8.1 -trf_path /N/soft/rhel8/repeatmasker/trf/4.09.1/trf -genome seq.fa -inharvest /N/scratch/befulton/repeatmodeler_test/RM_108867.MonMar251020042024/LTR_114100.MonMar251026312024/raw-struct-results.txt -noanno > LTR_retriever.log 2>&1
LTR_retriever failed to generate a file.  Please check /N/scratch/befulton/repeatmodeler_test/RM_108867.MonMar251020042024/LTR_114100.MonMar251026312024/LRET_114100.MonMar251026402024/LTR_retriever.log for details. at /geode2/soft/hps/rhel8/repeatmodeler/2.0.5/LTRPipeline line 693.

Observe the broken link to seq.fa in /N/scratch/befulton/repeatmodeler_test/RM_108867.MonMar251020042024/LTR_114100.MonMar251026312024/LRET_114100.MonMar251026402024

Try to reproduce the LTR_Retriever run:

/N/soft/rhel8/repeatmodeler/ltr_retriever/2.9.0/LTR_retriever -blastplus /N/soft/rhel8/repeatmasker/rmblastn/2.13.0/bin -cdhit_path /N/soft/rhel8/repeatmodeler/cdhit/4.8.1 -trf_path /N/soft/rhel8/repeatmasker/trf/4.09.1/trf -genome seq.fa -inharvest /geode2/home/u015/befulton/Quartz/repeatmodeler_test/RM_2755299.MonMar250925332024/LTR_2756415.MonMar250929242024/raw-struct-results.txt -noanno
Use of uninitialized value in numeric gt (>) at /N/soft/rhel8/repeatmodeler/ltr_retriever/2.9.0/LTR_retriever line 189.
rmhubley commented 3 months ago

I agree that this is problematic for debugging ltr_retreiver, however it makes it easier to debug LTRPipeline, although only in a minor way. I'll add this to the feature list for future releases.