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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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Error: cp: cannot stat *.retriever.scn.adj’: No such file or directory #133

Closed dmf445 closed 2 years ago

dmf445 commented 2 years ago

Hi shujun,

I have met this error when I ran LTR_retriver, The error as follow:

##########################
### LTR_retriever v2.9.0 ###
##########################

Parameters: -genome */ltr.fa -inharvest */ltr.fa.scn -repeatmasker /home/dell/miniconda3/envs/LTR/bin/RepeatMasker -trf_path /home/dell/miniconda3/envs/LTR/bin/trf

 CST    Dependency checking: All passed!
 CST    LTR_retriever is starting from the Init step.
 CST    Start to convert inputs...
                                Total candidates: 12800
                                Total uniq candidates: 12800

 CST    Module 1: Start to clean up candidates...
                                Sequences with 10 missing bp or 0.8 missing data rate will be discarded.
                                Sequences containing tandem repeats will be discarded.

        Usage: perl cleanup.pl -f sample.fa [options] > sample.cln.fa
        Options:
                -misschar       n       Define the letter representing unknown sequences; case insensitive; default: n
                -Nscreen        [0|1]   Enable (1) or disable (0) the -nc parameter; default: 1
                -nc             [int]   Ambuguous sequence len cutoff; discard the entire sequence if > this number; default: 0
                -nr             [0-1]   Ambuguous sequence percentage cutoff; discard the entire sequence if > this number; default: 1
                -minlen         [int]   Minimum sequence length filter after clean up; default: 100 (bp)
                -cleanN         [0|1]   Retain (0) or remove (1) the -misschar taget in output sequence; default: 0
                -trf            [0|1]   Enable (1) or disable (0) tandem repeat finder (trf); default: 1
                -trf_path       path    Path to the trf program

 17:32:46 CST    0 clean candidates remained

Error: cp: cannot stat *.retriever.scn.adj’: No such file or directory
 CST    No LTR-RT was found in your data.
 CST    All analyses were finished!

The result has no output file. Could you give me some advice?

THANKS!!!

dmf445 commented 2 years ago

I changed the genome and it seems to be working properly.

Alteroldis commented 10 months ago

Hi Shujun, I got the error also during RepeatModeler pipeline. But only on 2.9.7 version, not v2.9.6. Genome seqids:

gi-1 gi-2 Full command: /home/Tools/LTR_retriever-v2.9.7/LTR_retriever -repeatmasker /home/Tools/RepeatMasker -blastplus /home/Tools/RMBlast/bin -cdhit_path /usr/bin -trf_path /home/Tools/TRF/bin/trf -genome seq.fa -inharvest raw-struct-results.txt -noanno -threads 48

oushujun commented 10 months ago

@Alteroldis Please try again with the github version independent of RepeatModeler. Thanks!

zxd-alt commented 2 months ago

hi I got a problem either and I changed another genome but it still like this (cp:cannot stat 'DM8.fa.retriever.scn.adj':NO such file or directory). Could you help me? THANKS!