Frequently Asked Questions

The following are some frequently asked questions from our users. For information to help troubleshoot common problems see our troubleshooting guide.

EPI2ME Desktop Application

How do I check the version of EPI2ME Desktop I have installed?

Click on the settings cog in the left panel.

Does EPI2ME Desktop need an internet connection?

To deliver the best possible experience in delivering up-to-date bioinformatic analyses, EPI2ME Desktop requires an internet connection to download workflows the first time they are run. After workflows are downloaded, an internet connection is not typically required for further use. Some connectivity may be required for downloading biological reference data from, for example, NCBI.

What internet resources does EPI2ME Desktop need to access?

The application will attempt connections to the following domains: labs.epi2me.io, amazonaws.com, api.github.com, docker.io, docker.com, oxfordnanoportal.com.

How do I update the environment?

On starting the application users will be informed if an update is available either for the application itself or the tutorial environment. The environment can be updated at any time through the application by going to the settings cog on the left of the application and clicking check for updates. Updates to the application can also be downloaded from the EPI2MELabs website.

Can I use EPI2ME Desktop on my computing cluster?

Yes. Although you may require permissions from your IT administrators, and to check with them that a firewall will not block it’s access to external resources.

Can I install EPI2ME Desktop on my GridION or PromethION?

You may install and run EPI2ME Desktop on your device. Follow the Linux (Debian) installation instructions. EPI2ME Desktop will be included in future versions of the device software.

Running And Managing Workflows

Can I run workflows on my GridION or PromethION?

You may install and run EPI2ME Desktop on your device. Follow the Linux (Debian) installation instructions. EPI2ME Desktop will be included in future versions of the device software. Nextflow should not be run on from a command prompt on devices - the preinstalled version of Nextflow is intended for the sole use of MinKNOW.

Can I use data from other technologies?

EPI2ME Labs workflows are designed and optimised to work with Oxford Nanopore Technologies’ long-read sequencing. They will typically not produce optimal results with data from other sequencing technologies.

Can I run more than one workflow at a time?

Multiple workflows can in principle be run simultaneously. EPI2ME Desktop does not however monitor the total resource used by workflows it starts to ensure the system is not put under undue resource pressure: users should be aware that running many workflows simultaneously may affect system performance and stability. You can watch the status of running workflows by clicking the instances clock icon.

On GridION and PromethION sequencing devices, EPI2ME Labs workflows run with lower priority than MinKNOW and so data acquisition should not be affected.

Can HTML reports be viewed offline?

Yes, the scripts and styling required to view them are packaged within the files.

Where can I find a list of the expected output for each workflow?

There is a list of expected outputs for each workflow in the GitHub repository for each workflow, scroll down in the README to outputs.

How do I find the output location from running a workflow?

Click the open instance button in the workflow overview tab.

Where can I find example data files to test the workflows on my computer?

There are some available in the test_data directory of each github workflow repository. There are also some larger open data sets available here.

The workflow shows in EPI2ME Desktop as completed, but there was no output. What steps should I take next?

Click open instance, and see if there are any output files present. If not then it is likely an error with the platform. Please contact us.

The workflow I ran ended with an error, what steps should I take next? Which files are needed to send in with a support ticket?

Try to rerun the workflow, it will try to complete from where it failed. If the workflow fails again please contact us.

I would like to clear more disk space after running workflows, which files are safe to delete?

You can manually delete the work folder of a run, click open instance from the workflow overview page and manually delete the work folder. If you are completely finished with a workflow and no longer need any of the data you can delete the entire directory.

Do EPI2ME Labs workflows support barcoded data?

Most of our workflows do support barcoded data but not all. If a workflow has a sample sheet parameter, then it does support barcoded data.

To run with multiple barcodes, you should input a directory that contains subdirectories one for each barcode. Optionally a sample sheet can be included to replace barcodes with sample names in any output files.

eg. input directory structure

├── barcode01
│   ├── reads0.fastq
│   ├── reads1.fastq
│   └── reads2.fastq
├── barcode02
│   ├── reads0.fastq
│   ├── reads1.fastq
│   └── reads2.fastq
└── barcode03
    └── reads0.fastq

Sample sheet files should be laid out according to the MinKNOW sample sheet specification. For EPI2ME Labs workflows a file minimally needs the barcode and sample_id fields:

barcode,sample_id
barcode01,sample01
barcode02,sample02
barcode03,sample03

More about Workflows

Which file on a workflows github page provides a list of the tools used, their versions, and parameters to run the command?

Software versions used are listed in the reports generated by EPI2ME Labs workflows. The parameters used can be found by inspecting the workflow source code.

Where can I find the actual code and commands used by the workflows?

In the github repository for each workflow, you can see a list of programs used in the environment.yaml and you can examine the Nextflow scripts (files with then .nf extension). If you need more guidance understanding the code it might be worth looking at the nextflow documentation.