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

[dmf445]

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]

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

[Alteroldis]

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]

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

[zxd-alt]

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!