Citing DeepGE in your publication sustains the maintenance and improvement of this web server and keeps the infrastructure available to everyone.
Available in the near future, please stay tuned.
Moreover, please cite the specific paper(s) for the tool(s) you used. Citations are shown on each web server page.
If you have any questions, bug reports, or suggestions, please do not hesitate to contact deepge [at] nrp-nautilus.io after consulting the frequently asked questions below.
When reporting a bug, please include:
If you have suggestions for new models of sufficient interest and impact available (even those outside our group), we may be able to accommodate the community, as long as we are allowed to host the models. Please contact deepge [at] nrp-nautilus.io if you would like to include new external models in the DeepGE platform.
When a job fails, the log area on the status page will show a red "Job failed. Please check the logs above for details." banner, and the logs themselves often contain a block like this:
================================================================================ A job that stops here is usually a problem with the input rather than an error of the web server. The logs above will contain information about what went wrong. The inputs are likely too short / too long / incorrectly formatted, or there are no PAM sequences / other necessary sequence locations required for editing the gene(s). If the logs above instead name a missing module, file or device, then nothing about your input caused this -- please report it. ================================================================================
If you see that message, the most common causes are:
That block cannot see what actually failed, so it describes the usual case. If the logs name something missing on the server — a module, a file, a device — the input is not the problem and no amount of editing it will help; report it instead.
What to do: 1. Open the Help tab on the web server page for format requirements and screenshots. 2. Click the Load Example button to see a working input, then compare it with yours. 3. Make sure every required field is filled in.
If a job fails repeatedly with the same input, and you have verified the input is correct, then please report it to deepge [at] nrp-nautilus.io, including the persistent job link, logs, and inputs you used.
Note: Occasionally, a job fails for a temporary reason that has nothing to do with your input. This does not require anything from you — the job restarts by itself.
While the job is starting, the log area may show one of these messages:
Most predictions finish within a few minutes. However, jobs that evaluate a very large number of possible guide RNAs, or that perform genome-wide off-target searches, may take hours or even days in extreme situations. You can leave the page and return later using the same job link; the result will still be there for three months.
Note: Jobs may fail on the first attempt and restart by themselves, or wait a long time — over 30 minutes — before they start. Neither means anything is wrong with your input. If a job has not started after a long wait, submitting it again usually gets it running sooner.
Job results are automatically deleted three months after submission. Please download your results promptly using the Download Results button on each results page.