User: andrespara
andrespara • 10
- Reputation:
- 10
- Status:
- New User
- Location:
- Uruguay/UDELAR/F100
- Last seen:
- 7 hours ago
- Joined:
- 4 years, 1 month ago
- Email:
- a*********@gmail.com
Posts by andrespara
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... Could you do it? I am in the same situtation and can't turn a UCSC 100 genome alignment into multifastas or something manageable and these old questions are [almost] the only reference to the format.. ...
written 13 hours ago by
andrespara • 10
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... Hi Carla, could you resolve this? I am trying the same as you I think, I downloaded the 100 vertebrate genome form UCSC and I am trying to obtain that alignment as multifasta**s** so I can later add another set of cds form another animal. I was looking then to search for orthologous between animal 1 ...
written 13 hours ago by
andrespara • 10
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... Thanks, we abandoned that node for the moment and moved the work to another machine (a Desktop in fact). If/when I put more work on schedule with that grid an machines I will pay attention to that error and if it appears only for that node or somewhere else. Thanks! ...
written 7 months ago by
andrespara • 10
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... Thanks Adrian, we will try to reproduce the error in other machines, by the way those machines have Ubuntu 14.04 running so that might interfere with the analysis (I am pushing or asking for an upgrade ATM).
In the meantime another run in another Desktop machine outside the cluster was interrupted ...
written 8 months ago by
andrespara • 10
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... Is there some way to diagnose or confirm this? I used a small dataset (3 individuals) in case some unexpected collisions occurred. Thanks ...
written 8 months ago by
andrespara • 10
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... That particular node worked fine some months ago but along other more powerful nodes in a parallelization with open grid engine, I thought maybe something changed or maybe the parallelization is failing here [in the meantime I launched again a test with only 3 individuals and it also dropped to a si ...
written 8 months ago by
andrespara • 10
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... Dear all,
I am having problems running OMA, I am running it in a single machine/node to avoid errors or conflict with the open grid engine. Even when I use `OMA -c` first and then `OMA -n 9` the node drops to half that amount of processors in a few minutes and now a single processor is running.
A ...
written 8 months ago by
andrespara • 10
• updated
7 months ago by
Biostar ♦♦ 20
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Comment:
C: grid engine problem with OMA
... Thanks! I will try this ...
written 18 months ago by
andrespara • 10
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C: grid engine problem with OMA
... Hi again, I wonder if I could send the jobs to **only** certain nodes so I can start multiple OMA runs with different datasets in the same grid. We have several nodes called "ubuntu-node2" "ubuntu-node3" and so on.
I am currently launching OMA with that line `qsub -v NR_PROCESSES=100 -b y -j y -t 1 ...
written 18 months ago by
andrespara • 10
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C: grid engine problem with OMA
... When I try to execute "qsub start-oma.sh" it says
> qsub: Unknown option
bash start-oma.sh
works but starts only one process and with qstat I didn't notice any activity but maybe it is part of the intention of the script. ...
written 22 months ago by
andrespara • 10
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For Which are free options for running OMA in a cluster?
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