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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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Issue with bin/make_lib.pl #107

Closed RanZhou closed 2 years ago

RanZhou commented 2 years ago

Hi,

I got this error/warnings during module 2-5: "use" not allowed in expression at /apps/eb/LTR_retriever/2.9.0-foss-2019b/bin/make_lib.pl line 9, at end of line syntax error at /apps/eb/LTR_retriever/2.9.0-foss-2019b/bin/make_lib.pl line 9, near "use warnings use strict" Execution of /apps/eb/LTR_retriever/2.9.0-foss-2019b/bin/make_lib.pl aborted due to compilation errors. mv: cannot stat $genome.fasta.ltrTE.pass.tmp.clust: No such file or directory

Do I need to worry about this?

Thanks,

Ran

oushujun commented 2 years ago

Hi Ran,

Thank you for reporting. I have fixed this. Please update your software and try again.

Best, Shujun

RanZhou commented 2 years ago

Hey Shujun,

After that was fixed, I ran into some new issues: Use of uninitialized value in numeric gt (>) at /apps/eb/LTR_retriever/2.9.0-foss-2019b/bin/make_lib.pl line 48, line 1. Argument "motif:TGCA" isn't numeric in numeric gt (>) at /apps/eb/LTR_retriever/2.9.0-foss-2019b/bin/make_lib.pl line 48, line 1.

And in Module 6: Start to analyze truncated LTR-RTs...

ERROR: No such file or directory at /apps/eb/LTR_retriever/2.9.0-foss-2019b/bin/make_lib.pl line 11. mv: cannot stat ‘$gGenome.fasta.ltrTE.tmp.clust’: No such file or directory

Although the jos seems to be finished, but I'm not sure if these issues will impact the results.

Thanks,

Ran

oushujun commented 2 years ago

Hi Ran,

Something is wrong. You may need to test the installation with a small genome.

Best, Shujun

On Thu, Nov 11, 2021 at 12:50 PM RanZhou @.***> wrote:

Hey Shujun,

After that was fixed, I ran into some new issues: Use of uninitialized value in numeric gt (>) at /apps/eb/LTR_retriever/2.9.0-foss-2019b/bin/make_lib.pl line 48, line 1. Argument "motif:TGCA" isn't numeric in numeric gt (>) at /apps/eb/LTR_retriever/2.9.0-foss-2019b/bin/make_lib.pl line 48, line 1.

And in Module 6: Start to analyze truncated LTR-RTs...

ERROR: No such file or directory at /apps/eb/LTR_retriever/2.9.0-foss-2019b/bin/make_lib.pl line 11. mv: cannot stat ‘$gGenome.fasta.ltrTE.tmp.clust’: No such file or directory

Although the jos seems to be finished, but I'm not sure if these issues will impact the results.

Thanks,

Ran

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