User: dtejadamartinez

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Posts by dtejadamartinez

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Comment: C: Error ruining OMA "OneMachineParallelInfo"
... edited to add The cluster use Sun Grid Engine, I'm still trying to run the data, including the Toy example, but this error always comes up: Reading GO file... Segmentation fault (core dumped) Regards, ...
written 9 days ago by dtejadamartinez10
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Comment: A: Error ruining OMA "OneMachineParallelInfo"
... edited to add There is a moment where conversions seem ready but the file says: conversion.running before that I run again OMA and I get the next error and the run die all. line 18: ulimit: stack size: cannot modify limit: Operation not permitted only_run_dbconv := true Starting ...
written 10 days ago by dtejadamartinez10 • updated 10 days ago by genomax46k
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Error ruining OMA "OneMachineParallelInfo"
... Hi, Trying to run OMA on 2 different cluster. In one cluster, it ran up to 32%, in another one it is cut at the beginning and the conversions are not finished. But I get the same following error in both cases: 1523613044.955060 - 1 - [pid 22699]: Computing Orcinus_orca vs Bos_taurus (Part 95 ...
omastandalone oma written 11 days ago by dtejadamartinez10 • updated 1 day ago by adrian.altenhoff380
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TRANSDECODER v5.0.2 - nucleotide sequences with ambiguity characters S,R,W,K, Y
... Hello, I download 30 coding sequences genomes of different species from Ensembl or NCBI. In order to eliminate the transcripts and isoforms I used cd-hitest first and then I passed the files through TRANSDECODER. In TRANSDECODER v.5.0.2 I did step 1 and 3, but the final file **fasta.transdecoder ...
transdecoder written 5 weeks ago by dtejadamartinez10 • updated 5 weeks ago by lieven.sterck1.2k
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Answer: A: start OMA run - file.log
... Hi, thanks for the answer. I have all the sequences in nucleotides, and in the input I have InputDataType := 'DNA'; That's why I find it strange. It only happens with the final files thrown by TRANSDECODER. Cheers, Daniela ...
written 5 weeks ago by dtejadamartinez10
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start OMA run - file.log
... Hi, I have a question about the file.log when OMA start to convert the files. I download 30 coding genomes of different species from Ensembl or NCBI. In order to eliminate the transcripts and isoforms I used cd-hitest first and then I passed the files through TRANSDECODER. When I start running ...
oma omabrowser written 5 weeks ago by dtejadamartinez10
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Comment: A: OMA - without all vs all
... Thanks for your help, I think I would compute all vs all then. ...
written 4 months ago by dtejadamartinez10
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OMA - without all vs all
... I have a data set of 700 coding sequences (which I saved in a reference.fa file) and I need to obtain the orthology relationships (orthologous and paralogous) of these genes against 70 species. I have downloaded the genome cds from NCBI for each species. Now, is it possible to get only these compari ...
oma orthology written 4 months ago by dtejadamartinez10

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