User: adrian.altenhoff

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380
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Switzerland
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1 month, 3 weeks ago
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4 years, 5 months ago
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a***************@inf.ethz.ch

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Posts by adrian.altenhoff

<prev • 48 results • page 1 of 5 • next >
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Answer: A: Error, (in OrthologousMatrix) values cannot be ordered
... By commenting out the `InparalogTol` and `ParalogTol` parameters the two variables are undefined and numeric comparisons of expressions involving these two variables are no longer possible. You need to assign values to them, this should fix your problem. ...
written 9 weeks ago by adrian.altenhoff380
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Answer: A: OMA output does not match settings
... In OMA we integrate data from many different sources. So it's quite difficult to have a coherent, comprehensive set of cross-references. Because of this we add our internal OMA-IDs, which are the UniProt species codes + a number and fall back to those in case we cannot identify one of the canonical ...
written 12 weeks ago by adrian.altenhoff380
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Comment: C: how to resume an oma job using grid engine
... What do you mean exactly with resume? did you stop the process? or did oma terminate? in that case, you can simply resubmit it - it will continue from where it left off. ...
written 12 weeks ago by adrian.altenhoff380
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Answer: A: Error ruining OMA "OneMachineParallelInfo"
... From the output you mention I think the problem is due to a restriction on your system you modify the stacksize. Some function in OMA require a significant amount of recursions, so we try to increase the stacksize as much as possible (linux: ulimit -s unlimited; mac: ulimit -s hard). Your output i ...
written 12 weeks ago by adrian.altenhoff380
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Comment: C: grid engine problem with OMA
... Hi, seems like you could specify the hostnames with `-l`, see for example answer in to a similar question in here: https://stackoverflow.com/questions/19635895/run-a-job-on-all-nodes-of-sun-grid-engine-cluster-only-once ...
written 3 months ago by adrian.altenhoff380
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Answer: A: start OMA run - file.log
... Hi, it seems to me that you have an inconsistency between your input data and the parameters: From this output it looks to me that you specified in the `parameters.drw` file the `InputDataType := 'DNA';` but you provide protein sequences (which would make sense to use). In that case OMA would con ...
written 3 months ago by adrian.altenhoff380
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Answer: A: Bacterial known pathway - the easiest way to find and download 1:1 orthologs to
... As @Joseph Hughes points out, you will have to either use the REST API to search for the orthologs of your query genes and limit them to the gram-positive genomes (as far as my understanding goes these are essentially the Actinobacteria), or you parse the flat files that contain all the orthologs an ...
written 5 months ago by adrian.altenhoff380
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Comment: C: usage of OMA on a HPC cluster with slurm
... I don't understand where you checked. in home/.oma, HOME/sdau_ssli_1/.oma or somewhere else. It should be in a subfolder called ".oma" in your home directory. you should be able to see the files if you run `ls $HOME/.oma` in the slurm cluster. If this is the place where you stored them, please check ...
written 6 months ago by adrian.altenhoff380
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Answer: A: OMA: gene_function.gaf output file empty
... Hi, indeed, the documentation is missing an important information. Function prediction in OMA is done on transferring existing annotations within OMA groups. The annotations can currently only come from exported genomes (from the omabrowser https://omabrowser.org/export ). We will add this inform ...
written 6 months ago by adrian.altenhoff380
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Comment: C: usage of OMA on a HPC cluster with slurm
... no, it should be in your home/.oma folder. `ls ~/.oma/` should list those files ...
written 6 months ago by adrian.altenhoff380

Latest awards to adrian.altenhoff

Scholar 6 months ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Scholar 15 months ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Scholar 21 months ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Scholar 2.1 years ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Is this warning fatal in OMA
Scholar 2.2 years ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Scholar 2.3 years ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Scholar 2.4 years ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Is this warning fatal in OMA
Scholar 2.5 years ago, created an answer that has been accepted. For A: Gene Gain/loss + Duplication Tree
Scholar 2.6 years ago, created an answer that has been accepted. For A: Gene Gain/loss + Duplication Tree
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: What exactly is OMA doing here ?
Scholar 2.6 years ago, created an answer that has been accepted. For A: Gene Gain/loss + Duplication Tree

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