User: adrian.altenhoff

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770
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Switzerland
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Last seen:
17 hours ago
Joined:
6 years, 12 months ago
Email:
a***************@inf.ethz.ch

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Posts by adrian.altenhoff

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Comment: C: OMA Phase 2 stuck in "reading all vs. all" stage for 24 hours
... Hi Ilenia, 21 species should definitively work out for OMA. Depending on the size of the genomes, the 8k hours might not be too far off. if you have a hard time to get the jobs scheduled in the cluster because of the 8hrs, you should consider to requeue jobs that take too long by setting an timelimi ...
written 6 days ago by adrian.altenhoff770
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Comment: C: Downloading all-against-all precomputed for any number of species returns 504 Ga
... Hi, sorry just saw your message now. I regularly receive email to contact@omabrowser.org, I think it is working. you can also send a message to me on adrian.altenhoff@inf.ethz.ch. The reason for the limit is mostly storage requirements. So think I could also provide you with a Viridiplantae export ...
written 4 weeks ago by adrian.altenhoff770
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Comment: C: Downloading all-against-all precomputed for any number of species returns 504 Ga
... glad to hear, you're welcome! Cheers ...
written 4 weeks ago by adrian.altenhoff770
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Comment: C: Downloading all-against-all precomputed for any number of species returns 504 Ga
... Hi m3hdad, the problem seems to be solved. I could now export again a small test set. Please let us know in case you still experience some problems. Sorry for the inconvenience this has caused. Best wishes Adrian ...
written 4 weeks ago by adrian.altenhoff770
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Comment: C: Downloading all-against-all precomputed for any number of species returns 504 Ga
... Hi @m3hdad, thanks for letting us know. We're experiencing some problems with our backend cluster. I'll let you know here once it is fixed. Best wishes Adrian ...
written 4 weeks ago by adrian.altenhoff770
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Answer: A: Error running OMA standalone at HOG computation step
... Hi Gaurav, (hi Alberto) I had a look at the problem and it turns out that there are some proteins with a huge number of crossreferences in the fasta header. The csv module has a limit on the length of each field, which is exceeded by these proteins. The fix is quite simple, so you can actually do i ...
written 5 weeks ago by adrian.altenhoff770
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Comment: C: Error running OMA standalone at HOG computation step
... Hi Gaurav, yes, en email with a link would be fine. The relevant files would be the ManualSpeciesTree.nwk, Map-SeqNum-ID.txt and the whole subfolder PairwiseOrthologs (all in Output directory). If you can send me that as a tarball (maybe with wetransfer) to adrian.altenhoff@inf.ethz.ch. thanks a ...
written 5 weeks ago by adrian.altenhoff770
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Answer: A: Error running OMA standalone at HOG computation step
... Hi Gaurav, indeed, this looks quite strange. regarding your question to rerun only the HOG inference step, in case you run OMA standalone with -d 2 (a bit more verbose output) you should find the command to start the HOG computation step in the output look, just above the extract you showed. Otherw ...
written 5 weeks ago by adrian.altenhoff770 • updated 5 weeks ago by GenoMax94k
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Comment: C: Predicting Gene Ontology function in OMA for large datasets
... ups, you were right. there was a change in the API of one of the functions we used that no longer supports handling of gziped files. This should be solved now. Currently deploying the updated version, you should be able to finally use the gziped files in a couple of minutes. sorry for the problems t ...
written 7 weeks ago by adrian.altenhoff770
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Comment: C: Predicting Gene Ontology function in OMA for large datasets
... Hi, sorry about this. I forgot one instance where to change the settings. it should work now with files up to 50MB. Best Adrian ...
written 8 weeks ago by adrian.altenhoff770

Latest awards to adrian.altenhoff

Scholar 5 weeks ago, created an answer that has been accepted. For A: OMA error: Writing Part files to general cache area, not a specific dir
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: OMA error: Writing Part files to general cache area, not a specific dir
Scholar 3 months ago, created an answer that has been accepted. For A: OMA error: Writing Part files to general cache area, not a specific dir
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: OMA error: Writing Part files to general cache area, not a specific dir
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: OMA error: Writing Part files to general cache area, not a specific dir
Scholar 20 months ago, created an answer that has been accepted. For A: OMA error in stage 2 of 2 stage process
Scholar 21 months ago, created an answer that has been accepted. For A: OMA error in stage 2 of 2 stage process
Scholar 3.0 years ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Scholar 3.8 years ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Scholar 4.3 years ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Scholar 4.6 years ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Teacher 4.7 years ago, created an answer with at least 3 up-votes. For A: Is this warning fatal in OMA
Scholar 4.7 years ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Scholar 4.8 years ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Scholar 4.9 years ago, created an answer that has been accepted. For A: Is this warning fatal in OMA
Teacher 4.9 years ago, created an answer with at least 3 up-votes. For A: Is this warning fatal in OMA
Scholar 5.0 years ago, created an answer that has been accepted. For A: Gene Gain/loss + Duplication Tree
Scholar 5.1 years ago, created an answer that has been accepted. For A: Gene Gain/loss + Duplication Tree
Teacher 5.1 years ago, created an answer with at least 3 up-votes. For A: What exactly is OMA doing here ?
Scholar 5.1 years ago, created an answer that has been accepted. For A: Gene Gain/loss + Duplication Tree

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