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oushujun / LTR_retriever

LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5813529/
GNU General Public License v3.0
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Dependency checker looking in wrong directory for makeblastdb #166

Open benfulton opened 3 months ago

benfulton commented 3 months ago

I am running LTR Retriever as a part of RepeatModeler. RepeatModeler sets each dependency manually on the command line, including the -blastplus parameter. But LTR Retriever is looking in some other directory to find makeblastdb.

$ ls /N/soft/rhel8/repeatmasker/rmblastn/2.13.0/bin/makeblastdb
/N/soft/rhel8/repeatmasker/rmblastn/2.13.0/bin/makeblastdb
$ /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 -debug

Result

Mon Mar 25 10:51:25 EDT 2024    Dependency checking: Error: makeblastdb is not exist in the BLAST+ path /N/soft/rhel8/repeatmasker/rm/2.13.0/bin/!
oushujun commented 2 months ago

Hello,

I hope it's not too late. The path for -blastplus is directly passed to use makeblastdb. If you give the path /N/soft/rhel8/repeatmasker/rmblastn/2.13.0/bin via -blastplus, then LTR_retriever is expecting an executable /N/soft/rhel8/repeatmasker/rmblastn/2.13.0/bin/makeblastdb. You may want to check if that's available and executable. Somehow the error message suggest a different path given.

Shujun