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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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No such file or directory output_by_list.pl line 35 #36

Closed crisvives closed 5 years ago

crisvives commented 5 years ago

Hi Shujun, I am getting the following error: ERROR: No such file or directory at /usr/local/apps/eb/LTR_retriever/1.6-foss-2016b/bin/output_by_list.pl line 35.

The simplified command that I am using is this one: LTR_retriever -genome $genome_file -inharvest $genome.ltrharvest.scn -infinder $genome.ltrfinder.scn -nonTGCA $genome.ltrharvest.nonTGCA.scn > $genome_file.LTR_retriever.out

It seems that is missing $genome_file.nmtf.ltrTE, but while LTR-Retriever is running, the following files with names having "$genome_file.nmtf.ltrTE*" are generated:

$genome_file.nmtf.ltrTE.LTR Sa_scaffold.fa.nmtf.ltrTE.LTR.masked $genome_file.nmtf.ltrTE.LTR.ori.out Sa_scaffold.fa.nmtf.ltrTE.LTR.tbl $genome_file.nmtf.ltrTE.fa.cleanup Sa_scaffold.fa.nmtf.ltrTE.stg1 $genome_file.nmtf.ltrTE.LTR.cat Sa_scaffold.fa.nmtf.ltrTE.LTR.masked.cleanup $genome_file.nmtf.ltrTE.LTR.out Sa_scaffold.fa.nmtf.ltrTE.fa Sa_scaffold.fa.nmtf.ltrTE.pass.list

Thank you for your help! Cristina

oushujun commented 5 years ago

Hi Cristina,

Thanks for your error message. It seems that the expected files are put in an unexpected folder. you may move LTR_retriever/1.6-foss-2016b/bin to LTR_retriever/ and should solve the problem.

If not, just download a fresh version of LTR_retriever and copy over the LTR_retriever/path file, and you should be good.

Please let me know if you need further help.

Best, Shujun

crisvives commented 5 years ago

I could solve the problem by moving files in to LTR_retriever/ folder. Thanks for your help, Shujun!