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oushujun / EDTA

Extensive de-novo TE Annotator
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1905-y
GNU General Public License v3.0
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awk: fatal: cannot open file `genome.fa.mod.pass.list' for reading: No such file or directory #490

Closed Dorrie1041 closed 1 month ago

Dorrie1041 commented 1 month ago

I install by conda, and when I run the test, I got this error, Could you please help me deal with that issue? Thank you! Here is the error I got.

Invalid value for shared scalar at /$MY_PATH/miniconda3/envs/EDTA/share /LTR_retriever/bin/LTR.identifier.pl line 114, line 11. cp: cannot stat 'genome.fa.mod.retriever.scn.adj': No such file or directory awk: fatal: cannot open file `genome.fa.mod.pass.list' for reading: No such file or directory Warning: LOC list - is empty.

Error: Error while loading sequence Filter sequence based on TEsorter classifications. Unclassified sequences will also be output to the clean file. Usage: perl cleanup_misclas.pl sequence.fa.rexdb.cls.tsv Author: Shujun Ou (shujun.ou.1@gmail.com) 10/11/2019

mv: cannot stat 'genome.fa.mod.LTR.intact.fa.ori.dusted.cln.cln': No such file or directory mv: cannot stat 'genome.fa.mod.LTR.intact.fa.ori.dusted.cln.cln.list': No such file or directory cp: cannot stat 'genome.fa.mod.LTR.intact.raw.fa.anno.list': No such file or directory ERROR: No such file or directory at /clusterfs/jgi/groups/science/homes/dshen/miniconda3/envs/EDTA/share/EDTA/util/output_by_list.pl line 39.