Running a Screen

When a screen is initiated by the DIGS tool, a project-specific, relational database is created. This 'screening database' captures data generated by DIGS.

Initial screening run

Before running a screen for the first time, create the screening database (a one-off procedure), as follows:

./digs_tool.pl –m=1 –i=[path to control file]

Once the screening database is successfully created, a screen can be executed as follows:

./digs_tool.pl –m=2 –i=[path to control file]

Progress is written to the terminal, and can also be monitored by issuing SQL queries against the relevant screening database. A screen can be stopped at any time. The next time the tool is restarted, it will initiate screening at the point it left off.

Connecting to DB:  eve_1_parvoviridae
Created report directory
Path: './tmp/result_set_38612_1618435290'
Probe sequences:   22 amino acid FASTA sequences
Reference library: 39902 amino acid sequences
Targets:           1866 target files
Previous queries:  41052 previous queries
Skipped in set:    41008 (of 41052)
Searches to run    44

### Starting database-integrated genome screening

tblastn: 1: 'Eurynorhynchus_pygmeus' (GCA_003697955, low_coverage)
target: 'GCA_003697955.1_ASM369795v1_genomic.fna'
probe:  'NC_001401-AAV2_NS'

 # 2 matches to probe: NC_001401-AAV2, NS
 # 0 matches above threshold (excluded: 0 < length; 2 < bitscore)
 # done 1 of 44 queries (%2.27)

tblastn: 2: 'Hypophthalmichthys_nobilis' (HypNob1.0, low_coverage)
target: 'GCA_004193235.1_HypNob1.0_genomic.fna'
probe:  'NC_001401-AAV2_NS'

The first few lines of output report the properties of the probe, reference and target sequence libraries that compose the screen.

In addition, the status of the screen is reported - of all the individual BLAST searches that comprise the screen, how many have been performed, and how many are still outstanding.

Run with the -v (--verbose) option to see more detailed log output.

If screening is interrupted for any reason, simply restart the process. Screening will continue from the point at which the interruption occurred.

Running a screen in the background

Since similarity search-based screens can take hours or days to complete, you may want to run your screen 'in the background', particularly if you are running DIGS on a networked server that you connect to remotely. This can be done as follows. First start the digs_tool.pl as follows:

./digs_tool.pl –m=2 –i=[path to control file] > [path to a log file, e.g. screen.log]

Once this command has been executed, press Ctrl+Z and then type:

bg

You should then see this output:

./digs_tool.pl -i ctl/example_1_EVE.ctl -m=2 > screen.log &

To check progress on the backgrounded screen, view the log file. For example using:

tail screen.log