2 votes
Accepted

Error while using E-utilities on slurm HPC

501 Protocol scheme 'https' is not supported (LWP::Protocol::https not installed) indicates that a specific perl module is missing. If indeed your edirect ...
vkkodali's user avatar
  • 1,266
2 votes

How to run Jupyter script on Slurm HPC

This is a bash script (#!/bin/bash) and you try to run python in it. You should save your python script (e.g. in "myscript.py") and call it within your bash script. Maybe first try to see if ...
jeremy's user avatar
  • 143
1 vote
Accepted

bsub with -M and -hl a good idea?

What this question appears to be about is capping the RAM usage on a node within a shared HPC. Being 'nice' on an HPC is very honourable indeed, it is however the system administrators jurisdiction. ...
M__'s user avatar
  • 12.3k
1 vote
Accepted

Multiple values for memory resources shown when Snakemake is run

You have defined mem_gb but not mem_mb in your resource configuration file. You can set them to same value by adding something ...
user324810's user avatar
  • 1,115
1 vote
Accepted

How to get the external (cluster) job id and not internal snakemake job id in cluster log files?

bsub supports some filename placeholders using a percent sign, like %J for the LSF job ID, so you can use that: ...
Jesse's user avatar
  • 947
1 vote

repophlan script to download bacterial genome

UPDATE 2: new log posted take-home message: I think it is working, it's just that a few errors happen sometimes when downloading things from big databases. It looks like there are a few warnings or ...
Maximilian Press's user avatar
1 vote

no result from heat map WGCNA

If you've copied over from some of the WGNCA tutorials you might have additionally copied the sizeGrWindow command - it's caused some of my plots to disappear. ie: ...
Jack Gisby's user avatar
1 vote

no result from heat map WGCNA

The plot is probably being drawn to a device that you cannot view on a cluster. If you're using the plotNetworkHeatmap function, say, try something like this: ...
Ram RS's user avatar
  • 2,311
1 vote
Accepted

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

There are two approaches you can take: There's a --conda-create-envs-only option that you can use to exit after creating the envs. You should get information about ...
Devon Ryan's user avatar
  • 19.6k

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