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Hello,
I'm having an issue with running the lifton software. I'm running it on an HPC environment using 100GB memory and a computer node that has 2000 cores. The below bash script has the command I…
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Hi there,
I was testing LiftOff and LiftOn to see which one is "best" for genome annotation. I was looking at some RefSeq genomes, lifting the brown-headed cowbird and red-winged blackbird onto the…
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Hi
There is a problem when I using `Lifton` to lift-over the annotation from the reference to another same species.
I got `miniprot` installed on my machine already and settled in environment vari…
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Hello all,
There seem to be quite a few race conditions if one runs lifton in parallel. A project I'm working on requires running lifton from several dozen source annotations to several hundred ref…
kdm9 updated
2 months ago
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Hi all,
I am a beginner in bioinformatics and I encountered a problem with the LiftOn command. It cannot find the tool miniprot because I installed miniprot in a different folder, not within the co…
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Hi, thank you for the tool, I am very excited to try it and compare the results from liftoff.
However, I am getting a gffutils error at the stage after miniprot:
```
>> Creating liftoff annotati…
jolbi updated
4 months ago
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Solving environment: failed
PackagesNotFoundError: The following packages are not available from current channels:
- lifton
Current channels:
- https://conda.anaconda.org/bioconda
-…
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Dear,
I'm trying to use OMArK to assess the quality of a genome annotation and to be able to compare multiple ones later.
However, whenever I try to run OMArK with the command `omark -f killi_lift…
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Hello,
I've been having issues running Liftoff. It's taking days to run and then terminates. I'm running it on an HPC environment using 100GB memory and a computer node that has 2000 cores. The bel…
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Hi,
First of all, thank you for this wonderful tool.
I attempted to run a command to call somatic variants, but unfortunately, the command failed.
Could you please suggest a way to troubleshoot …