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FAQ
If you experience a kill status during a diamond search, it could be that you are running out of memory space. --block-size/-b is the main parameter for controlling the program’s memory and disk space usage. detectEVE as a default has a larger -b value for increased performance. Reduce this value in the config.yaml file for reducing memory use.
In theory, yes, however detectEVE is not optimized yet to distinguish between retrotransposable elements or retroviral elements and does not have additional search criteria for target genes, such as gag and pol. As of now, all retroviral EVEs are categorized as low confidence hits in our output.tsv file. Several specialized approaches have been developed for the identification of retroviral elements such as RetroSeq, or ERVcaller.
We have specifically chosen to exclude viral dsDNA virus-derived from the default analysis in detectEVE. While it is theoretically possible to use detectEVE for these detections, the differentiation between partial sequences of exogenous dsDNA viruses in genome assemblies and viral integrations remains challenging. Several specialized approaches have been developed for the identification of prophages in complete microbial genomes (e.g. Phage_Finder or Prophinder, detectEVE, however, provides an open framework for future developments which can include the detection of all EVE types.