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Comment: Split chromosome into smaller fragments to save memory when build xg and gcsa in
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Jordan M Eizenga
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750
GCSA2 indexing is fairly demanding on disk space, so that can happen. I would generally recommend having 1-2 TB of disk availability if you…
Comment: how to start
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shelkmike
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If you plan to become a professional bioinformatician, I don't recommend the approach suggested by Joe and Yura Grabovska (learning bioinfo…
Comment: vg input and output files
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GenoMax
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Have you looked at this page: https://github.com/vgteam/vg/wiki/Basic-Operations
There is a pipeline illustration on this page that shows …
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ATpoint
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To me knowledge, ensembl approach means that you run several tools and then run some sort of filtration and classification approach to deci…
Comment: vg input and output files
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Pierre Lindenbaum
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vg is a toolkit containing different tools. What are you talking about when you want to use 'input' and 'output' files.
Comment: Parabricks : Number of GPUs requested (2) is more than number of GPUs (0) in the
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Pierre Lindenbaum
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Thanks for the suggestion. I've got `--gres=gpu:2` in my sbatch header (so I imagine it doesn't change much things (?) ).
I also suspect a…
Comment: Split chromosome into smaller fragments to save memory when build xg and gcsa in
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李经纬
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Thank you. Even if I build the XG index after some modifications, the building of gcsa failed even on a single chromosome. Even though I h…
Comment: Parabricks : Number of GPUs requested (2) is more than number of GPUs (0) in the
by
Mensur Dlakic
★
29k
For posterity, here is `nvidia-smi` output for our cluster:
```
+-------------------------------------------------------------------------…
Answer: Parabricks : Number of GPUs requested (2) is more than number of GPUs (0) in the
by
Mensur Dlakic
★
29k
How often do we get a chance to help @yokofakun after all the help Pierre has provided? I feel like we have to make a serious effort here.
…
Comment: DiffBind error when calling dba.count
by
Irene
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0
I am having the same issue with the same situation, so i do not understand what could be the problem...i do not know if you finally figure …
Comment: Parabricks : Number of GPUs requested (2) is more than number of GPUs (0) in the
by
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@genomax I'm using the 'GPU' queue of my cluster (SLURM). The very same config was used with another parabrick subtool and I got not probl…
Comment: Parabricks : Number of GPUs requested (2) is more than number of GPUs (0) in the
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Are you running this under a job scheduler? Is there a separate partition for the GPU's/are they accessible to the scheduler?
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Are the batches biological replicates?
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shelkmike
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If you want to save time at the cost of having a lesser understanding of how bioinformatic programs work, you may study through the BioStar…
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