Two Nuc_translator.pm modules #185

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1. brianjohnhaas commented on Sep 21, 2023

   

   brianjohnhaas

   on Sep 21, 2023 via email

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   Hi Ayse, The tools should be separately using their own PerlLib directories and not cross-contaminating or otherwise interfering with each other. If someone has tampered with the PASA software structure or code, I'd suggest reinstalling it. best, ~b

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   On Thu, Sep 21, 2023 at 2:56 PM atengertrolander ***@***.***> wrote: Hi there, I recently asked our HPC cluster to install Pasa. I kept running into the following error: - [Wed Sep 20 21:24:28 2023] Running CMD: cat ./trinity_combined/trinity_transcripts.fa.clean ../stringtie/stringtie_c3_j3.gtf.fasta > __all_transcripts.fasta - [Wed Sep 20 21:24:28 2023] Running CMD: /gpfs/data/icelake-apps/software/gcc-12.1.0/pasapipeline/2.5.3/pasa-plugins/transdecoder/TransDecoder.LongOrfs -t __all_transcripts.fasta Undefined subroutine &Nuc_translator::get_genetic_codes called at /gpfs/data/icelake-apps/software/gcc-12.1.0/pasapipeline/2.5.3/pasa-plugins/transdecoder/TransDecoder.LongOrfs line 34. Error, cmd: /gpfs/data/icelake-apps/software/gcc-12.1.0/pasapipeline/2.5.3/pasa-plugins/transdecoder/TransDecoder.LongOrfs -t __all_transcripts.fasta died with ret 65280 No such file or directory at /gpfs/data/icelake-apps/software/gcc-12.1.0/pasapipeline/2.5.3/PerlLib/Pipeliner.pm line 187. Pipeliner::run(Pipeliner=HASH(0x1b90680)) called at /apps/software/gcc-12.1.0/pasapipeline/2.5.3/Launch_PASA_pipeline.pl line 1061 When I reported it to our cluster, they informed me that the function "get_genetic_codes" did not exist in the module. I then found the correct (I think) module in github ( https://github.com/TransDecoder/TransDecoder/blob/3c77d07564997c2884634421a432b4412bfad933/PerlLib/Nuc_translator.pm) which does have the get_genetic_codes function defined. But it seems there are two Nuc_translator.pm modules. See ( https://github.com/TransDecoder/TransDecoder/blob/master/PerlLib/Nuc_translator.pm). I just wanted to let you know that this might be a problem, especially for HPC clusters that have to select one to take precedence whenever the module is loaded. Best, Ayse — Reply to this email directly, view it on GitHub <#185>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX5PBF24HB6UMDNDTL3X3SEVDANCNFSM6AAAAAA5CAEBKQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

   -- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>
2. atengertrolander commented on Sep 21, 2023

   

   atengertrolander

   on Sep 21, 2023

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   Hi Brian,
   Thanks for your quick reply. I'll ask that Transdecoder and PASA be installed separately.
   Thanks!
   Ayse
3. atengertrolander commented on Sep 21, 2023

   

   atengertrolander

   on Sep 21, 2023

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   One more question, can pasa and transcoder then be loaded at the same time? Our cluster admin is worried that one code set will still take precedence over than other.
4. brianjohnhaas commented on Sep 21, 2023

   

   brianjohnhaas

   on Sep 21, 2023 via email

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   They can be loaded simultaneously but no perlllib paths should be adjusted. Only make the software accessible via the PATH setting

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   On Thu, Sep 21, 2023 at 4:17 PM atengertrolander ***@***.***> wrote: One more question, can pasa and transcoder then be loaded at the same time? Our cluster admin is worried that one code set will still take precedence over than other. — Reply to this email directly, view it on GitHub <#185 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKXYYCKGFY4YHFZ4OVPTX3SOEBANCNFSM6AAAAAA5CAEBKQ> . You are receiving this because you commented.Message ID: ***@***.***>