Frequently asked questions¶
1) I installed APRICOT using pip and I am trying to test the software using the script run_example.sh. Why does it shows me error messages about the missing files?
- APRICOT contains the library and scripts to run the analysis, however it requires additionally databases and tools to run the analysis. Although you do not need to install these resources to run an example (for testing purpose), you still need a set of data to mimic these data sources. You can get these example datasets in the git repository or download it from Zenodo.
- The path for these files can be defined in the script run_example.sh
using the variable
$DEMO_FILES.
2) I installed APRICOT using pip and I am trying to test the software using the script run_example.sh. Why can’t I run the subcommand ``annoscore`` and ``addanno``?
- The subcommand
annoscorerequires the toolneedlefrom the EMBOSS pakage andaddannouses Psortb and RaptorX. Hence, in order to run these subcommands of APRICOT a complete file-system (tool and database dependencies of the software) is required, which is supplied through APRICOT’s Docker image. Alternatively see the script apricot_minimum_required_files.sh for manual installation. - Please check the documentation or this video tutorial for the usage of these subcommand.
- The complete list of software requirements can be seen here, alternatively see the Dockerfile.
3) What are the options to give query proteins for the analysis?
- The query proteins can be provided as UniProt ids (-ui), gene ids/name (-gi), fasta files (-fa), taxonomy id to restrict the search of query to a specific species (-tx) and flag -P for a complete proteome analysis of the given taxonomy.
4) What are the rules for the input for domain selection terms?
- There is no specific rule for the selection of these terms in order to provide to the software for the collection of domains of interest. The choices of the term ranges from biological or MeSH terms (for example, term “RNA-bind” to select all the domains that mentions this term in its annotation) to specific domain class name or Pfam domain id/name (for example, “RRM” or “RNA-recognition-motif”).
- Terms containing multiple keywords can be provided using a hyphen (-) and “#” can be used before or after the term as a wild-card. Please see the documentation for other specific detail.
5) Why do I get an error message ‘Error: Unknown argument: “i”’ when running ‘rpsblast’ in the subcommand `predict`?
- This error appears when the user is using ‘rpsblast’ command from an older version of NCBI-BLAST package. The options -query (query protein file), -db (database) and -out (output path) are used instead of -i, -d and -o, which were the corresponding flags in the older version.