Test Data

Before continuing to running EnTAP, it is advised to do a test run to ensure that everything is properly configured. There should be no errors in the test run. The test data resides within the /test_data directory of the main EnTAP directory. This will walk you through configuring a database for DIAMOND (if you haven’t already done so) and executing EnTAP with and without frame selection.

Before we begin, make sure that the paths in the configuration file are correct. Since we are running the configuration stage, EnTAP will check to make sure you have the other databases downloaded (which should have been done prior to this). To begin the test, execute the following command to configure the test DIAMOND database:

EnTAP --config -d /test_data/uniprot_sprot.pep --out-dir /test_data --ini path/to/ini_file

This should finish very shortly without any errors and you should find a uniprot_sprot.dmnd file within the /test_data directory.

Next up is verifying the main execution stage! Once again, first ensure that the Config File has all of the correct paths. We are going to check an execution with and without frame selection. If you are not going to use frame selection, you may skip this test!

Note

The following tests will take longer as they will be testing the entire pipeline and running against the larger EggNOG database.

To test EnTAP with the frame selection portion of the pipeline, execute the following command:

EnTAP --runP -i /test_data/nucleotide_trinity.fnn -d /test_data/bin/uniprot_sprot.dmnd --ini path/to/ini_file

To test EnTAP without frame selection, execute the following command:

EnTAP --runP -i /test_data/protein_transdecoder.faa -d /test_data/bin/uniprot_sprot.dmnd --ini path/to/ini_file

These should run without error and you should have several files within the created /entap_outfiles directory.

If any failures were seen during the above executions, be sure to go through each stage of installation and configuration to be sure everything was configured correctly before continuing. If you have no received any errors, the following pages will go through the main annotation portion of the pipeline.

Note

The ini file may be distributed to each user to ensure they are pointing to the correct database and execution paths.