Troubleshooting

Content of this page:

How to Change the Temp-Folder Location of OmicsBox

OmicsBox can handle big data-sets, but it needs plenty of free disk space in the systems temporary files folder. If you run into troubles with shortage of disk space, follow this guide to manually change the location of the folder for OmicsBox temporary files to e.g. another partition. The preferences dialog shown on the right allows you to change the temporary folder location, please make sure to restart OmicsBox after changing this setting in order to make it effective.

For further information on how to change the tempfolder location of OmicsBox, please visit: https://www.biobam.com/how-to-change-blast2go-tempfolder/

How to Set Max-Memory of OmicsBox

OmicsBox automatically reserves up to 50% of the available system memory (i.e. RAM), which is fine in most cases. However, sometimes and especially on Linux, this can lead to excessive disk swapping and will slow down OmicsBox. Follow this guide to manually change the maximum amount of memory OmicsBox will be allowed to use. The preferences dialog shown on the right allows you to change the temporary folder location, please make sure to restart OmicsBox after changing this setting in order to make it effective.

On Linux distributions like Ubuntu it is recommendable to change the vm.swappiness parameter from 60 to 1: https://help.ubuntu.com/community/SwapFaq#What_is_swappiness_and_how_do_I_change_it.3F

For further details, please visit: https://www.biobam.com/how-to-change-blast2go-heap-memory/

OmicsBox with Sleep, Power-Save or Suspension Mode?

OmicsBox needs to be connected to the internet to run the jobs on the Cloud.
To run tools e.g. overnight please make sure the computer does not go into power save mode which, depending on the configuration, might disconnect the internet or put the computer to sleep. If there are internet connection problems or if the computer goes into sleep mode the data cannot be sent or retrieved from the Cloud. Thus there is the need to have a good internet connection and disable the computer sleep mode. Below you can find instructions on how to do this, although you can find more detailed information on the webpage of each operating system provider.

Windows 10 

Modify Power & sleep options in Settings

Open Settings and click on System icon.

System -> Preferences -> Power Management

On AC Power Tab, Put computer to sleep when inactive for: "Never"

Choose Power & sleep option from the left panel and make the changes accordingly to Screen and Sleep option.

For more information visit the following webpage.

MacOS

The option is available in Apple () menu > System Preferences, then click Energy Saver.
(In the Power Adapter tab if you are using a laptop) Select "Prevent computer from sleeping automatically when the display is off"
or drag the "Computer sleep" slider to set the sleep mode to Never if there is one.

For more information visit Apple support.

Linux - Ubuntu

This option is available in System > Preferences > Power Management in Ubuntu.
On AC Power Tab, Put the computer to sleep when inactive for: "Never"

For more information visit Ask Ubuntu webpage.

Using Google Drive, One Drive or other cloud files streaming services with OmicsBox?

Our recommendation is NOT to use file locations which are synchronised/stream in the cloud.

OmicsBox has experienced issues with projects getting corrupted because of the files being synchronized while the tool is modifying them.
We recommend having a copy of the files locally and not open them directly via streaming from the cloud storage provider. If you really want to use the files from the cloud storage folder make sure that the files are available locally and that the synchronization is paused for this folder during the analysis.

Note: If you decide to use the Desktop or Documents folder, make sure that these are not part of the cloud storage. One Drive, for instance, synchronizes both these folders into the cloud by default. Otherwise, just use another path. A good place to copy the files is the OmicsBoxWorkspace folder available in the user's home folder.