database file (rds.tsv) not readable about platon HOT 13 CLOSED

Hi!
Is the zenodo link to the database not working because of this issue?
Thank you for developing this tool btw!
Looking forward to use it.
Best

from platon.

Hi @Lneffe , @Aliceall ,
thanks for using Platon. May I ask which database version you downloaded and use? I think there might be a mismatch between the installed Platon version (v1.1.0) and the database version.

We introduced some major changes in v1.2.0 which therefore is not compatible anymore with older database versions.

I highly recommend to update both (tool & db) to the latest versions, .i.e. v1.3.1 and https://zenodo.org/record/3751774 since we made some major improvements.
Best regards!

from platon.

Hello @oschwengers !

Thank you for the advice.
It seems that I am not able to update the platon tool using the command
conda update platon
in the specific environment that I created for platon.
I also tried deinstalling the version and running again
conda install -c conda-forge -c bioconda -c defaults platon
but ended up with version 1.1. still.

`The following packages will be SUPERSEDED by a higher-priority channel:

platon ::platon-1.3.1-py_0 --> bioconda::platon-1.1.0-py_1`

How can I get version 1.3.1 via the conda channel (my version is conda 4.8.3)?
I am working in a shared server environment and do not have permissions for pip/github installation.

Many thanks in advance,
looking forward to use the promising tool!

from platon.

Hello @Lneffe ,
unfortunately, I cannot reproduce this error. I'm also using conda 4.8.3 and conda install -c conda-forge -c bioconda -c defaults platon in a fresh environment works as expected ending in a working platon v1.3.1 installation. Maybe there is a wrong configuration in your conda setup/channels?

If you do not have sudo priviledges on your system, you could also try pip with the --user option together with git clone?

git clone [email protected]:oschwengers/platon.git
cd platon
python3 -m pip install --user platon

from platon.

Hello @oschwengers !
The issue was with the python version and conda configuration.
I now used python version 3.8.3 in a completly new environment and installed the the tool incl. database.
A first test run was succesfully completed as well.

Best regards!

from platon.

You're welcome, nice that it's working, now.
Best regards!

from platon.

Thank you @oschwengers!
I have conda 4.8.3, python 3.7, platon 1.3.1
I have installed everything following your instructions but when I get to this: platon --db ./db genome.fasta
it says is not readable.
Am I doing something wrong?
Thank you!

from platon.

Hi @Aliceall ,
ok, just to go through this step by step:

1. You're able to execute platon --help without any errors?
2. Did you use an existing assembly in fasta format instead of just genome.fasta?

If yes, could you then please execute platon with the --verbose flag, open a new issue (as I guess this might be unrelated to the initial issue) and provide me with the resulting log file, so I can check the details?
Thanks and best regards!

from platon.

Thank you.
the help message executes without errors. I hadn't try to run anything yet, I was just installing and following your steps. I will try now with my spades assembly and let you know how it goes.
Thanks

from platon.

It worked perfectly!
thank you very much! Have a great day

from platon.

Nice, you're welcome!
Best regards!

from platon.

from platon.

Hi @Aliceall ,
I'm not quite sure which file you mean by "called contigs". Platon writes 5 distinct files:

• "<prefix>.chromosome.fasta": all contigs classified as chromosomal
• "<prefix>.plasmid.fasta": all contigs classified as plasmid-born
• "<prefix>.tsv": a tab-separated file copying the STDOUT
• "<prefix>.json": a JSON file containing all results
• "<prefix>.log": a log file with detailed (internal) information - mainly for debugging purposes

The PCLA_* numbers are identifiers from the NCBI prokaryotic proteins clusters: https://www.ncbi.nlm.nih.gov/proteinclusters/browse

Your specific PCLA hit for PCLA_3224486 refers to the traN gene: https://www.ncbi.nlm.nih.gov/proteinclusters/?term=PCLA_3224486

The main application for Platon is to separate plamid-borne from chromosomal contigs for further analysis. An overview on the plasmid-borne contigs is printed to STDOUT and the <prefix>.tsv file. The <prefix>.json file contains all detailed information in a machine readable format.

I hope I could clarify your questions. Please, do not hesitate to keep asking if you have any further questions - but may I kindly ask you to open a new dedicated issue as the initial problem of this one is solved? This helps others with equal issues to find existing answers.

from platon.