SplitsTree command line mode

Question

[Matteo Schiavinato]

Hi all,

I am trying to integrate SplitsTree4 in a pipeline I'm working on. The manual explains quite clearly how to structure this:

• an input file
• a command file with operations

I have followed these instructions and made a command file that looks like this:

begin SplitsTree;
SAVE FILE=test.phy.nex
EXPORTGRAPHICS format=SVG file=network.test.svg
QUIT
end;

And then I run the command like this:

/../SplitsTree \
--input test.phy \
--commandLineMode \
--commandFile cmd_file.txt \
--version \
--verbose

The program begins, starts reading the input file, tells me N. of sequences, length and datatype (automatically inferred), but then just stucks there forever.

Anyone experienced this? Ideas on what I could have done wrong / be missing? No error is reported, it is just stuck. Copy-pasting the terminal print-out where it is stuck:

SplitsTree4 (version 4.14.6, built 26 Sep 2017)
Attempting to import in format: PhylipSequencesInterleaved
TAXA
Read TAXA:
    7 taxa
Read CHARACTERS:
CHARACTERS
    7 sequences, each 50, datatype: dna

Answer 1

[Matteo Schiavinato]

I answer my own question for future readers:

If you define --input <FILE that will work only without command line. That is for loading a file to a GUI instance directly. To load a file from command line, it has to be declared via the command file, using for example LOAD FILE, or IMPORT FILE (see manual for this).