User: andrespara

gravatar for andrespara
andrespara10
Reputation:
10
Status:
New User
Location:
Uruguay/UDELAR/F100
Last seen:
5 months, 3 weeks ago
Joined:
4 years, 7 months ago
Email:
a*********@gmail.com

Posts by andrespara

<prev • 21 results • page 1 of 3 • next >
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Comment: C: Which file should I use to retrieve CDs following the GenBank Assembly link? No
... Thanks I will try some of these tools. ...
written 6 months ago by andrespara10
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Which file should I use to retrieve CDs following the GenBank Assembly link? No RefSeq available.
... Hi, I want to gather CDs from NCBI or Ensembl. For some species there is NO curated RefSeq assembly, only the link to "ftp directory for GenBank assembly" There I found GBFF files AND genomic.fna files. If I **only** want CDs like I usually recover in RefSeq links, which one is the correct one? I ...
ncbi assembly refseq gbff cds written 6 months ago by andrespara10
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Comment: C: Adding sequences to preexisting MAF alignment
... 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 6 months ago by andrespara10
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Comment: C: Adding sequences to preexisting MAF alignment
... 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 6 months ago by andrespara10
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Comment: C: OMA core dumped error in a single node/machine
... 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 14 months ago by andrespara10
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Comment: C: OMA core dumped error in a single node/machine
... 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 14 months ago by andrespara10
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Comment: C: OMA core dumped error in a single node/machine
... Is there some way to diagnose or confirm this? I used a small dataset (3 individuals) in case some unexpected collisions occurred. Thanks ...
written 14 months ago by andrespara10
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Comment: C: OMA core dumped error in a single node/machine
... 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 14 months ago by andrespara10
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OMA core dumped error in a single node/machine
... 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 ...
oma orthology written 14 months ago by andrespara10 • updated 14 months ago by Biostar ♦♦ 20
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Comment: C: grid engine problem with OMA
... Thanks! I will try this ...
written 2.0 years ago by andrespara10

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Popular Question 2.3 years ago, created a question with more than 1,000 views. For Which are free options for running OMA in a cluster?

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