Trinotate: incorrect paths to perl scripts looking for /util/admin

[Rob W.]

Hi Brian,

I'm at the beginning of the Trinotate pipeline but the initial Trinotate --create command keeps failing. This is the error I get:

Trinotate --db myTrinotate.sqlite --create --trinotate_data_dir /storage/home/rpw5414/scratch/trinotate/databases/
-CREATING myTrinotate.sqlite and populating data dir: /storage/home/rpw5414/scratch/trinotate/databases/
* [Thu Jan  4 13:40:19 2024] Running CMD: /storage/home/rpw5414/.conda/envs/bioinfo/bin/util/admin/Build_Trinotate_Boilerplate_SQLite_db.pl TrinotateBoilerplate
Can't exec "/storage/home/rpw5414/.conda/envs/bioinfo/bin/util/admin/Build_Trinotate_Boilerplate_SQLite_db.pl": No such file or directory at /storage/home/rpw5414/.conda/envs/bioinfo/lib/perl5/site_perl/Pipeliner.pm line 176.
Error, cmd: /storage/home/rpw5414/.conda/envs/bioinfo/bin/util/admin/Build_Trinotate_Boilerplate_SQLite_db.pl TrinotateBoilerplate died with ret -1 No such file or directory at /storage/home/rpw5414/.conda/envs/bioinfo/lib/perl5/site_perl/Pipeliner.pm line 187.
Pipeliner::run(Pipeliner=HASH(0x55fe55b87ee0)) called at /storage/home/rpw5414/.conda/envs/bioinfo/bin/Trinotate line 439
main::run_Trinotate_create("myTrinotate.sqlite", "/storage/home/rpw5414/scratch/trinotate/databases/") called at /storage/home/rpw5414/.conda/envs/bioinfo/bin/Trinotate line 248

When I run Build_Trinotate_Boilerplate_SQLite_db.pl by itself, I get this:

/storage/home/rpw5414/.conda/envs/bioinfo/bin/Build_Trinotate_Boilerplate_SQLite_db.pl Trinotate
* [Thu Jan  4 13:46:32 2024] Running CMD: wget "https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz" -O uniprot_sprot.dat.gz
--2024-01-04 13:46:32--  https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz
Resolving ftp.uniprot.org (ftp.uniprot.org)... 128.175.240.195
Connecting to ftp.uniprot.org (ftp.uniprot.org)|128.175.240.195|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 661965214 (631M) [application/x-gzip]
Saving to: 'uniprot_sprot.dat.gz'

uniprot_sprot.dat.gz                100%[=================================================================>] 631.30M  1.30MB/s    in 7m 33s  

2024-01-04 13:54:06 (1.39 MB/s) - 'uniprot_sprot.dat.gz' saved [661965214/661965214]

* [Thu Jan  4 13:54:06 2024] Running CMD: /storage/home/rpw5414/.conda/envs/bioinfo/bin/util/EMBL_swissprot_parser.pl uniprot_sprot.dat.gz Trinotate
Can't exec "/storage/home/rpw5414/.conda/envs/bioinfo/bin/util/EMBL_swissprot_parser.pl": No such file or directory at /storage/home/rpw5414/.conda/envs/bioinfo/lib/perl5/site_perl/Pipeliner.pm line 176.
Error, cmd: /storage/home/rpw5414/.conda/envs/bioinfo/bin/util/EMBL_swissprot_parser.pl uniprot_sprot.dat.gz Trinotate died with ret -1 No such file or directory at /storage/home/rpw5414/.conda/envs/bioinfo/lib/perl5/site_perl/Pipeliner.pm line 187.
Pipeliner::run(Pipeliner=HASH(0x55eba86077a0)) called at /storage/home/rpw5414/.conda/envs/bioinfo/bin/Build_Trinotate_Boilerplate_SQLite_db.pl line 131

So these commands keep dying with "No such file", and it seems that they are searching for /path/to/.conda/envs/bioinfo/bin/util/admin/ when all the scripts are actually installed to /path/to/.conda/envs/bioinfo/bin/. My /bin/ doesn't have a "util/admin/" directory.

 

Is there a way to manually circumvent this problem? Maybe just making a /util/admin directory and copying in the necessary files? 

Was there a problem during installation perhaps? I tried installing Trinotate in a fresh conda environment and they still installed to the /bin/.

Thanks for your help,

Robert

[Brian Haas]

Hi Rob,

I don't directly support the conda installations - others do that separately/independently.   Can you try just pulling down the latest release code and running it directly?   Better yet, if you can use the singularity image, it comes with (almost) everything needed:
https://github.com/Trinotate/Trinotate/wiki/TrinotateViaSingularity

best,

Brian

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Brian J. Haas
The Broad Institute
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[Rob W.]

Hi Brian,

Thanks for that info. My university's cluster has Singularity, so I've downloaded that image and run the command on the wiki page: singularity shell -e trinotate.simg. 

When you say "for convenience, set the TRINOTATE_HOME environmental variable to where Trinotate is installed in the image", where exactly would that be? Is it the same in every image? I tried running just "Trinotate" and nothing came up. Is the TRINOTATE_HOME going to be the directory that contains the trinotate.v4.0.2.simg? And once I'm in the Trinotate shell, should I just try running the commands that I did above (after navigating to the same working directory as above)?

I have a little experience with Singularity, but only a little, so I appreciate the clarification.

Robert

[Brian Haas]

Hi Rob,

 

When you're in the Trinotate shell with the singularity image, then just execute the command:

  export TRINOTATE_HOME=/usr/local/src/Trinotate

and then when you run:

     $TRINOTATE_HOME/Trinotate   

it should give you the usage info.

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