User: adrian.altenhoff

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300
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Switzerland
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1 week, 2 days ago
Joined:
3 years, 9 months ago
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a***************@inf.ethz.ch

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Posts by adrian.altenhoff

<prev • 23 results • page 1 of 3 • next >
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Answer: A: OMA error message
... Hi I think these are two issues. I observed that on some SGE setups you need to set the environment variables outside the submission script, prior to calling the qsub command. The problem about the stacksize is related to the cluster setup. You should try to set the stacksize to the maximal possibl ...
written 10 weeks ago by adrian.altenhoff300
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Comment: C: OMA sequences with no Xs
... Hi Dimar, I don't understand your question. as far as I can see there are many cdna sequences with the 'unknown' character in the latest release. please indicate more precisely which file, from where and when you are working with. ...
written 4 months ago by adrian.altenhoff300
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Answer: A: OMA warning about mapping to a clade
... When doing function propagation in OMA, we try to limit the taxonomic range to which we propagate functional annotations. This is done by checking in which clades existing function annotations occur. Now, if you did not export at least some genomes from OMA (with the export functionality in http://o ...
written 6 months ago by adrian.altenhoff300
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Answer: A: OMA WARNING: took too long (>1200 sec) to find clusters
... Hi Tauana, these warnings indicate that you are analysing big gene families. The top-down algorithm to infer HOGs gives up after a certain time (you can specify in the parameters file) and continues with a lower level. The effect is that for these gene families you won't be able to go back to very ...
written 6 months ago by adrian.altenhoff300
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Answer: A: OMA, Error in PropagateFunctionByGroup, invalid arguments in intersect (Mac OS)
... Hi I'm one of the developers of OMA standalone. Obviously, this should not happen. About these two runs: did you analyse the same dataset, i.e. the same genomes? what were the two platforms? one linux box, what about the other (failing) platform? The bug seemed to have occurred during the GO func ...
written 8 months ago by adrian.altenhoff300
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Answer: A: OMA Error code
... Hi, OMA standalone downloads only the GeneOntology (www.geneontology.org/ontology/gene_ontology.obo) from the web if needed (i.e. if DoGroupFunctionPrediction in parameter.drw is set to true and the file hasn't been downloaded before). From the error, it seems that you were either not connected to ...
written 8 months ago by adrian.altenhoff300
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Answer: A: OMA, GOdata/Wget error
... The error you observed is caused by a ubuntu specific problem. we took the chance to release a bug-fix version ([1.1.2][1]). Thanks for reporting. [1]: http://omabrowser.org/standalone/ ...
written 12 months ago by adrian.altenhoff300
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Comment: C: Error when running oma-standalone v1.0.6: Error, (in RangeOfChunk_iterator) sequ
... yes, that is a good point. thanks, will include! ...
written 16 months ago by adrian.altenhoff300
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Answer: A: Error when running oma-standalone v1.0.6: Error, (in RangeOfChunk_iterator) sequ
... Hi Javier, yes, there is a hard limit of currently slightly over 100k AA. The value of the constant doesn't really matter too much. For the next release, I will increase this number to 200k. Do you think that would be enough? In the meanwhile, you can either skip these very long sequences, truncate ...
written 16 months ago by adrian.altenhoff300
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Answer: A: Error when running OMA on PBS with job array
... Hi, which version of OMA standalone are you using? On version (I think it was 1.0.5) was buggy in that respect that the conversion was done by all running processes if started with a scheduler. The multiple process write to the same file and create garbage. In your case, the ascii character 0x00 wa ...
written 17 months ago by adrian.altenhoff300

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 12 months ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Scholar 16 months ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Is this warning fatal in OMA
Scholar 17 months ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Scholar 19 months ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Scholar 20 months ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Is this warning fatal in OMA
Scholar 21 months ago, created an answer that has been accepted. For A: Gene Gain/loss + Duplication Tree
Scholar 22 months ago, created an answer that has been accepted. For A: Gene Gain/loss + Duplication Tree
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: What exactly is OMA doing here ?
Scholar 22 months ago, created an answer that has been accepted. For A: Gene Gain/loss + Duplication Tree

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