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Questions tagged [hpc]

Acronym for "high performance computing"

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31 views

Load balancing numerous single-threaded processes with Snakemake on the grid

I'm familiar with running Snakemake in a DRMAA-enabled grid environment. (Most often, I write Python programs as wrappers and invoke the workflow via Snakemake's Python API.) Typically, I'm running ...
2
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0answers
59 views

Snakemake fails because it cannot create logs inside a read-only Singularity Container

I am using Snakemake from inside a Singularity container. Because of that, the directory that Snakemake wants to log to cannot be created, and I get an ...
0
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0answers
41 views

Why I get Singularity error when I try to run MAKER Genome Annotation on HPC?

I need to run MAKER genome annotation for my assembly file on HPC and I'm new to this. When I try to do that I get this error. ...
0
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1answer
27 views

Error while using E-utilities on slurm HPC

I keep getting the error while using E-utilities on Slurm HPC, could you suggest how I can resolve it? SCRIPT: ...
1
vote
2answers
192 views

How to run Jupyter script on Slurm HPC

Now jupyter installed on the server and I am using below code to plot the rarefaction plot but I am still getting some error. could you please suggest how I can get rid of it? ...
0
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1answer
74 views

repophlan script to download bacterial genome

I am trying to donwload the microbial genome using the repophlan_get_microbes.py (https://github.com/SegataLab/repophlan) but now it is running more than 10 days and still not finished on slurm HPC. ...
1
vote
2answers
43 views

no result from heat map WGCNA

I have created a heat map using WGCNA using R. But the heat map command is not showing the plot and there is no error. I have a large number of modules and traits. I am not sure if that is the reason. ...
0
votes
1answer
33 views

How to run a one-time 'setup' step for amrfinder in snakemake using conda

I'm trying to add amrfinder running within conda to a snakemake workflow, working on a slurm HPC. The first time you run amrfinder, you have to run ...