User: adrian.altenhoff
adrian.altenhoff • 460
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Posts by adrian.altenhoff
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... Hi,
the error is raised if the file in Cache/DB/Echinops_telfairi.db has been changed since it has been created (right in the beginning from the the fasta file). differences are based on computing a hash value from the file, so any modification of the file (for example changing an protein ID, etc) ...
written 6 days ago by
adrian.altenhoff • 460
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... Hi Andre,
I had another look into your original error and tried to figure out if the value the structure points to could actually be some meaningful data, but it turns out that this is very unlikely. It's certainly not a string value and unlikely to be even a floating point value. Let me know in ca ...
written 24 days ago by
adrian.altenhoff • 460
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... Hi
your command should indeed start 100 jobs of oma standalone in parallel. however the cluster configuration specifies how much resources a job should be allocated by default if not otherwise specified. I assume that your configuration allows to use a lot of resources and hence it will only start ...
written 29 days ago by
adrian.altenhoff • 460
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Comment:
C: Best way running OMA using SLURM
... There is a default parameter file that is used in case there are no arguments ...
written 29 days ago by
adrian.altenhoff • 460
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Comment:
C: OMA cannot evaluate boolean
... no worries. good to hear! ...
written 29 days ago by
adrian.altenhoff • 460
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... ok, thanks for the update. Ubuntu14.04 should in principle work fine - we have tested OmaStandalone on this setup and used it also for some analysis. Feel free to get back to me (also via omabrowser contact email) if you get stuck. But I agree that it could be simply a hardware problem of that node. ...
written 29 days ago by
adrian.altenhoff • 460
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... Dear andre,
can you reproduce this error also on a different compute node? The error indicates indeed a very general memory problem. Did you for example reserve enough resources through the scheduler? If you can reproduce it, the best way would be to make your concrete dataset available to me (best ...
written 29 days ago by
adrian.altenhoff • 460
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4
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Answer:
A: OMA cannot evaluate boolean
... Hi Thomas
the error indicate that some parameter is undefined or alternatively the input data might be not in the right format. Could you please rerun OMA Standalone with higher verbosity level, i.e. by running it as `OMA -c -d 3` which should produce a more informative error message in general.
...
written 29 days ago by
adrian.altenhoff • 460
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... could it be that that node has too little memory? I haven't seen this type of error before, and it is a bit weird that with a single process it works. Those processes do not even communicate with each other...
Adrian ...
written 4 weeks ago by
adrian.altenhoff • 460
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... Hi,
I assume you refer the tree in Output/EstimatedSpeciesTree.nwk (or since OmaStandalone 2.3.0 also in phyloxml format). The numbers are branch lengths in PAM (point accepted mutations).
This tree is a relative crude estimate of the underlying species tree but usually good enough for us to inf ...
written 10 weeks ago by
adrian.altenhoff • 460
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