Question: OMA error: Writing Part files to general cache area, not a specific dir
0
gravatar for moranr
3.0 years ago by
moranr250
Ireland
moranr250 wrote:

Hi,

I am rerunning a pervious OMA run, changing some of the genomes. I added the files to the DB and it created the new db, tree and map in the Cache DB. However, no folder in the AllAll for the new genomes were created. When I run OMA , i get something like this :

[pid  36623]: Computing  vs  (Part 1 of 177). Mem: 0.712GB

Usually it tells me what is being compared.

This part file is left just floating in the AllAll dir, and not put into a specific dir within the AllAll dir.

Have you any idea of what I have done wrong here to create this situation ?

Thanks, R

homology oma • 824 views
ADD COMMENTlink modified 3.0 years ago by adrian.altenhoff520 • written 3.0 years ago by moranr250
3
gravatar for adrian.altenhoff
3.0 years ago by
Switzerland
adrian.altenhoff520 wrote:

Dear Ray,

This sounds very strange. I suspect you haven't used an existing genome name for the fasta file or some non-ascii characters (or started the name with a blank), did you? Do the Cache/DB files (the .db at least) look similar to the other genome databases?

Did you maybe also change the version of OMA at the same time?

I suggest that you start OMA with -d 4 option on a single process. please verify in the log that all the Cache/DB/*db files are read that you expect without any error.

If nothing helps, please contact me directly with a minimal example, e.g. only the new genomes and you parameter file.

Best wishes Adrian

ADD COMMENTlink written 3.0 years ago by adrian.altenhoff520
0
gravatar for natasha.sernova
3.0 years ago by
natasha.sernova3.4k
natasha.sernova3.4k wrote:

What version of OMA do you use?

See their manual again:

http://omabrowser.org/standalone

The problem may be memory lack.

I'm running OMA on 50 processors of 1Tb node with 80 processors as a whole (600Gb),

I'm using University cluster.

I use OMA for 70 bacterial genomes. The parallel way never worked for me. How do you run the program?

Send a letter to authors, new version is not as simple as an old one.

Actually, they will see OMA-tag and will contact you, don't worry.

I had to modify parameters.drw - file several times to have a correct output.

BTW, look at your parameters.drw-file. How do these lines look like?

if you want to recompute everything from scratch everytime the script

is run, set the following parameter to false.

ReuseCachedResults := true;

false is a default. In your case the line should look like line above.

OMA is not a trivial program, so there can be some other reasons.

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by natasha.sernova3.4k
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