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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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Can't exec "-misschar" #91

Closed xiaoyezao closed 3 years ago

xiaoyezao commented 3 years ago

Hi Shujun,

I encountered the following error message:

Can't exec "-misschar": Permission denied at /PARA/pp427/app/ltr_retriever-2.9.0/bin/cleanup.pl line 61.
Use of uninitialized value $tandem in substitution (s///) at /PARA/pp427/app/ltr_retriever-2.9.0/bin/cleanup.pl line 62.

and many others:

Use of uninitialized value $lLTR_start in numeric lt (<) at /PARA/pp427/app/ltr_retriever-2.9.0/bin/make_gff3.pl line 55, <List>
Use of uninitialized value $rLTR_end in numeric lt (<) at /PARA/pp427/app/ltr_retriever-2.9.0/bin/make_gff3.pl line 55, <List> l
Use of uninitialized value $chr in concatenation (.) or string at /PARA/pp427/app/ltr_retriever-2.9.0/bin/make_gff3.pl line 63,

Are these serious problems? How to fix them?

Tao

xiaoyezao commented 3 years ago

Following the issues mentioned above, the job seems finished successfully, but with more warnings (see the attached log file)

What's wrong going here? Any suggestions?

slurm-4637302.out.txt

oushujun commented 3 years ago

Have you tried on a simple genome or simplify the sequence names? -Shujun

On Thu, Apr 29, 2021 at 1:19 PM xiaoyezao @.***> wrote:

Following the issues mentioned above, the job seems finished successfully, but with more warnings (see the attached log file)

What's wrong going here? Any suggestions?

slurm-4637302.out.txt https://github.com/oushujun/LTR_retriever/files/6396431/slurm-4637302.out.txt

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