Corrected gene treesΒΆ

All outputs from SCORPiOs are stored in a folder named SCORPiOs_jobname/ (with the jobname as specified in the configuration file).

The main output is the SCORPiOs-optimized gene trees. Gene trees are provided as a single file in NHX format. We explain in the next section how to visualize SCORPiOs corrections.

The run commands generate:

  • SCORPiOs_example/SCORPiOs_output_0.nhx for the simple run,

  • SCORPiOs_example/SCORPiOs_output_2_with_tags.nhx for the iterative run.

Outputs are suffixed with a digit representing the iteration number. This number is set to 0 in simple mode and starts at 1 in iterative mode.

Note

NHX tags are added to the corrected gene trees:

  • NEW in 1.3.0 (iterative mode only), corrected WGD nodes CORR_ID_WGD=Y,

  • leaves of corrected subtrees are tagged with CORR_ID_WGD=ID,

  • leaves rearranged to reinsert subtrees are tagged with MOVED_ID_WGD=ID;

where WGD will be replaced by the name of the corrected WGD and members of the same corrected subtree will be given the same ID.

For instance, two leaves, with the tag CORR_ID_Clupeocephala=1 for one and CORR_ID_Clupeocephala=2 for the other, belong to two different subtrees corrected for the Clupeocephala WGD.

In iterative mode, correction tags are additionaly suffixed with the iteration number of the first correction (i.e CORR_ID_Clupeocephala_1=1).

Warning

Please note that MOVED_ID_ is currently not supported in the final output in iterative mode. However, they are stored in individual, by iteration, corrected trees (see the entry save_tmp_trees of the Configuration file), in the exact same format as in the non-iterative run. Corrections at each iteration can be visualized with SCORPiOs custom tree visualization script, using all available drawing options (see Tree visualization).

Some intermediary outputs are also stored in different sub-folders of SCORPiOs_jobname/. Please see the section on Intermediary outputs for a detailed description.

In addition, SCORPiOs writes statistics on key steps of the workflow to the standard output. Thus, to separate output statistics from Snakemake logs, you can run:

snakemake --configfile config_example.yaml --use-conda --cores 4 --scheduler=greedy >out 2>err

or

bash iterate_scorpios.sh --snake_args="--configfile config_example.yaml --cores 4 --scheduler=greedy"  >out 2>err