Issue with bin/make_lib.pl

[RanZhou]

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]

Hi Ran,

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

Best,
Shujun

[RanZhou]

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]

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 — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub <#107 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNX4NCKHZJGXEYTSFT4I6LULQGBFANCNFSM5HWLMOGQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.