mmseqs_clustering_update.smk error: Invalid database read for database data

[mhyleung]

Dear all

We are currently testing AGNOSTOS on our system, but breaking it based on the different snakemake sub-runs in agnostos-wf/db_update/rules/

In the steps within mmseqs_clustering_update.smk, in the very last task, we are currently getting the following error:

/agnostos-wf/bin/mmseqs createtsv /agnostos_test/db_update/mmseqs_clustering/seqDB /agnostos_test/db_update/mmseqs_clustering/seqDB /agnostos_test/db_update/mmseqs_clustering/cluDB /agnostos_test/db_update/mmseqs_clustering/cluDB.tsv --threads 28
createtsv /agnostos_test/db_update/mmseqs_clustering/seqDB /agnostos_test/db_update/mmseqs_clustering/seqDB /agnostos_test/db_update/mmseqs_clustering/cluDB /agnostos_test/db_update/mmseqs_clustering/cluDB.tsv --threads 28

MMseqs Version:                         2f1db01c5109b07db23dc06df9d232e82b1b4b99-MPI
First sequence as representative        false
Target column                           1
Add full header                         false
Sequence source                         0
Database output                         false
Threads                                 28
Compressed                              0
Verbosity                               3

Invalid database read for database data file=/agnostos_test/db_update/mmseqs_clustering/seqDB_h, database index=/agnostos_test/db_update/mmseqs_clustering/seqDB_h.index
getData: local id (4294967295) >= db size (427306981)

We are actually testing AGNOSTOS based on the database that also contains the expanded sequences from the TARA ocean works (FigShare link) that contains the expanded eukaryotic plankton predicted gene sequences. Could that be related? Thanks

Marcus

[ChiaraVanni]

Hi Marcus,
It seems to be a problem with the clustering database. We haven't integrated new data in this database yet. I will let you known once is fixed.

Thank you for using AGNOSTOS!

Chiara

[mhyleung]

Hi Chiara

Thanks for the response. Would you suggest us using the seed database, or is there a slightly more recent database that has been formatted for AGNOSTOS use? Thanks

Marcus

[ChiaraVanni]

Hi Marcus,
the other two DBs publicly available at the moment are the seed and the seed+giant viruses, so I guess it depends on which are your scientific questions. I'm already running a test clustering-update on the database with the TARA eukaryotes, hopefully I can identify the problem and fix it soon.

Chiara

[mhyleung]

Hi Chiara

I presume the database containing the seed+giant viruses is this one? https://figshare.com/articles/dataset/agnostosDB_a42ac58a-20200715/13251743

Cheers

Marcus

[ChiaraVanni]

Yes.

Cheers

Chiara