ribosomal_models not available

[paulzierep]

It seems that the ribosomal_models are not available from the provided link anymore:

wget ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipeline-5.0/ref-dbs/rfam_models/ribosomal_models/RF*.cm \
  ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipeline-5.0/ref-dbs/rfam_models/ribosomal_models/ribo.claninfo \
  -P ribosomal 

Error:

--2023-04-03 14:57:04--  ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipeline-5.0/ref-dbs/rfam_models/ribosomal_models/RF*.cm
           => ‘.listing’
Resolving ftp.ebi.ac.uk (ftp.ebi.ac.uk)... 193.62.193.138
Connecting to ftp.ebi.ac.uk (ftp.ebi.ac.uk)|193.62.193.138|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done.    ==> PWD ... done.
==> TYPE I ... done.  ==> CWD (1) /pub/databases/metagenomics/pipeline-5.0/ref-dbs/rfam_models/ribosomal_models ... 
No such directory ‘pub/databases/metagenomics/pipeline-5.0/ref-dbs/rfam_models/ribosomal_models’.

Could you please update the link, we are trying to run the pipeline locally.

[KateSakharova]

Hello @paulzierep,
Thank you for your report!

Some folders were compressed on FTP. I fixed it and changed command for ribosomal models. README was updated.

MGnify team kindly ask not to run pipeline locally. It takes a big efford, computer power, patience (and a bit of magic with CWL/Toil runners:) ). Please, use our resource https://www.ebi.ac.uk/metagenomics/ , submit your data and we will do it for you much quicker and provide you all the results.

Best,
Kate

[paulzierep]

@KeteSakharova maybe as a bit more context, I am working for the Galaxy Team in Freiburg. We might try to add some parts of the MGnify pipeline to galaxy (some of the tools but also potentially the complete workflow). I think this was also discussed to some extent previously. Feel free to contact me zierep@informatik.uni-freiburg.de if you like to learn more about this.

Best,
Paul

[RZ9082]

Hello @KeteSakharova,

I am running the CMsearch on the small data sample https://www.ebi.ac.uk/metagenomics/analyses/MGYA00570790#taxonomic . I am using the same version and command used the pipline-v5, also the ribosomal models linked in README.
Unfortunately I do not get the same output as MGnify.

My output:

The MGnify SSU-seqs:

I am missing "ERR2407324.2-10333.Pue.782.huma-1-1-SSU_rRNA_eukarya" in my output.

Could you kindly assist me in identifying any potential mistakes I may have made during the execution of the CMsearch tool?

Best,
Rand