Questions tagged [hpc]
Acronym for "high performance computing"
14
questions
4
votes
2
answers
87
views
Running bwa mem and samtools in one script on a linux cluster
I am trying to write a script that will run this line from https://github.com/kmceres/Mbovis_pangenome/blob/main/Parameter_file.md:
...
- 109
3
votes
2
answers
85
views
Running multiple sequence using spades.py on an HPC
I am trying to run a batch script to assemble sequences using the spades.py command on HPC. I tested the script with one sequence (1 forward and 1 reverse read) and this worked. I have 100 sequences ...
- 109
1
vote
0
answers
28
views
Assessing the quality of an assembly
I am trying to run a script that assess the quality of a transcriptomic assembly, a de novo assembly using a tool called Transrate. To install the tool I followed the prompts in https://bioconda....
- 163
4
votes
2
answers
142
views
How can I override the time limit set by my administrator on SLURM using snakemake?
I am running PGS Calculator on a High-Performance Computer with the operating system GNU/Linux.
I have an executable script named pgs_hack.slurm containing the following code:
...
- 325
1
vote
1
answer
72
views
bsub with -M and -hl a good idea?
I have been submitting my snakemake pipeline to a node-shared high performance computer (HPC) via bsub the following way:
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- 383
1
vote
1
answer
178
views
Multiple values for memory resources shown when Snakemake is run
I am running a Snakemake (V7.14.0) pipeline on the cluster and provided resources in a resource config file like:
threads:
tool1: 4
mem_gb:
tool1: 12
Point ...
- 383
1
vote
1
answer
124
views
How to get the external (cluster) job id and not internal snakemake job id in cluster log files?
Background I am using snakemake and I want to add the external (cluster) jobid to my cluster output and error log files. Below is my shell script.
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- 383
1
vote
0
answers
51
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 ...
- 5,090
3
votes
0
answers
426
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 ...
- 141
0
votes
1
answer
45
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:
...
- 393
1
vote
2
answers
436
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?
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- 393
0
votes
1
answer
170
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.
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- 393
1
vote
2
answers
58
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. ...
- 111
0
votes
1
answer
81
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 ...
- 217