Error in Running TransDecoder.LongOrfs line 16 #175
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oh, I thought I had gotten rid of that dependency.
You can just run:
cpanm install URI::Escape
and that should solve the problem. Let me know if that gives you any
trouble.
best,
~b
…On Tue, May 9, 2023 at 3:02 PM hollybpalk ***@***.***> wrote:
Hello,
I downloaded the newest release of TransDecoder-v.5.7.0. I ran the command:
./TransDecoder.LongOrfs -t
~/transcriptome_data/final_assemblies/abdomin.clean.mrna.fa
However, I receive the following error:
Compilation failed in require at ./TransDecoder.LongOrfs line 16. BEGIN
failed--compilation aborted at ./TransDecoder.LongOrfs line 16.
When I attempt the make test, I receive an error
Can't locate URI/Escape.pm in @inc
How do you recommend fixing the error? Thank you!
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Brian J. Haas
The Broad Institute
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Thank you so much! I ran that command and received the following output: However, when I tried the make test command again, I still received the error Is there an error on my end? Or are there any more steps I should take? |
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hmm..... You can try this, which might work better:
perl -MCPAN -e shell
install URI::Escape
exit
Let's see if that works.
best,
~b
…On Tue, May 9, 2023 at 3:12 PM hollybpalk ***@***.***> wrote:
Thank you so much! I ran that command and received the following output:
install is up to date. (0.01) URI::Escape is up to date. (5.19)
However, when I tried the make test command again, I still received the
error
Can't locate URI/Escape.pm in @inc (you may need to install the
URI::Escape module)
Is there an error on my end? Or are there any more steps I should take?
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Hello, I am receiving that same error for some reason. When I ran your suggestion, it ran and completed. I am running jobs on a university HPC, so I am not sure if that is causing the problem. Thank you so much. |
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I see. It could be that the HPC server that it's running on has a
different perl installation and is missing the module.
I could create a new release that has the URI::Escape dependency
removed... Sound good?
…On Tue, May 9, 2023 at 4:01 PM hollybpalk ***@***.***> wrote:
Hello, I am receiving that same error for some reason. When I ran your
suggestion, it ran and completed. I am running jobs on a university HPC, so
I am not sure if that is causing the problem. Thank you so much.
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I see, I thought maybe that was a possibility. Yes that would be excellent, Thank you so much!!! |
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hmm.... It looks like version 5.7.0 should have the dependency removed.
I wonder if it's an issue with a perl lib path.
if you run:
env | grep PERL
what does it return?
best,
~b
…On Tue, May 9, 2023 at 4:08 PM hollybpalk ***@***.***> wrote:
I see, I thought maybe that was a possibility. Yes that would be
excellent, Thank you so much!!!
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It does not return anything. |
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The mystery deepens.
Can you try going to a new working directory, pulling this code:
https://github.com/TransDecoder/TransDecoder/archive/refs/tags/TransDecoder-v5.7.0.tar.gz
un-tar'ing it, and then try running the TransDecoder.LongOrfs that's in
there? (with no arguments.... just see if it runs).
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I apologize for the late response, I received this error: |
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well, at least it's not URI::Escape this time.
Try installing the Data::Dumper module via cpanm or the perl -MCPAN -e
shell way.
Hope that helps,
~brian
…On Wed, May 10, 2023 at 11:15 AM hollybpalk ***@***.***> wrote:
I apologize for the late response, I received this error:
Can't locate Data/Dumper.pm in @inc <https://github.com/inc> (you may
need to install the Data::Dumper mo dule) ***@***.*** <https://github.com/inc>
contains: /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/p
erl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5
/usr/share/perl5) at ./TransDecoder.LongOrfs line 9.
BEGIN failed--compilation aborted at ./TransDecoder.LongOrfs line 9.
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Hello,
I downloaded the newest release of TransDecoder-v.5.7.0. I ran the command:
./TransDecoder.LongOrfs -t ~/transcriptome_data/final_assemblies/abdomin.clean.mrna.faHowever, I receive the following error:
Compilation failed in require at ./TransDecoder.LongOrfs line 16. BEGIN failed--compilation aborted at ./TransDecoder.LongOrfs line 16.When I attempt the make test, I receive an error
Can't locate URI/Escape.pm in @INCHow do you recommend fixing the error? Thank you!
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