User: Andrew Watson
Andrew Watson • 40
- Reputation:
- 40
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- New User
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- United Kingdom
- Last seen:
- 1 month ago
- Joined:
- 6 years, 11 months ago
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about me
Posts by Andrew Watson
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... Hi Adrian,
Great, thanks for the information. I had thought/hoped that they might scale differently.
I was mainly checking to get an idea of a starting point to discuss with the HPC admins. A single core with high memory and for a longer than usual wall-time doesn't fit neatly into any of their ...
written 4 weeks ago by
Andrew Watson • 40
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... I am trying to estimate memory requirements to run the final steps OMA standalone (after the ALL-vs ALL) on a HPC (slurm), without HOG inference.
From the benchmarks in the manual, the suggested formula is 400MB * pow(nr_genomes, 1.4).
This works for the described metazoan dataset (60 metazoas hav ...
written 4 weeks ago by
Andrew Watson • 40
• updated
4 weeks ago by
adrian.altenhoff • 700
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Answer:
A: phylobayes mpi error
... I was under the impression that Phylobayes only accepts .phy files so did not think of this until I asked around.
If anyone is still having this problem then it can be easily worked around by inputting the sequence in .nexus format, so that the data type is explicitly stated. ...
written 4.5 years ago by
Andrew Watson • 40
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Comment:
C: phylobayes mpi error
... We are having the same error. Has this been resolved?
We have been running pb_mpi on two linux servers successfully for some time now.
The error occurred with a new alignment, but we went back to check some older ones we have successfully used in the past with pb_mpi and came up against the same e ...
written 4.5 years ago by
Andrew Watson • 40
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... Very useful thanks! Used it on my own dataset (sorry to bump an old thread but still very handy)
...
written 6.7 years ago by
Andrew Watson • 40
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... Just to confirm I have been managed to solve this in case anyone else encounters the problem.
As I have annotated against a reference genome I have some cases where zero expression has been detected under either of the conditions I am studying.
I used the matrix of the fpkm values (from fpkmMatrix ...
written 6.9 years ago by
Andrew Watson • 40
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... Hi all,
I am having trouble with the expressionBarplot function on cummeRbund and was wondering if anyone could help me.
I want to look at the expression plot of a manually created geneset. I have worked through several already without any problems, but this particular set is pulling up the below ...
written 6.9 years ago by
Andrew Watson • 40
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Popular Question
6.0 years ago,
created a question with more than 1,000 views.
For Cummerbund Expressionbarplot Na/Infinite Error
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