Installation not possible

[bheimbu]

Hi @caseywdunn,

I cannot install sowhat. Is it to outdated? I work on a cluster without admin privileges.

Any help is highly appreciated. Here is the error.log.

Cheers Bastian

[josephryan]

Can you try this for me and see if it works?

Create a conda environment called sowhat

conda create sowhat
conda activate sowhat
conda install -c conda-forge perl-app-cpanminus
conda install -c anaconda wget
conda install -c bioconda seq-gen
cpanm Statistics::R

Download a fresh distribution.

wget https://github.com/josephryan/sowhat/archive/refs/tags/v1.0.tar.gz
gzip -dc v1.0.tar.gz | tar -xvf -
cd sowhat-1.0

Install sowhat

cd sowhat-1.0/
perl Makefile.PL
make
make test
make install

[bheimbu]

Hi @caseywdunn,

still getting the same error…

$ make test
PERL_DL_NONLAZY=1 "/home/uni08/bheimbu/miniforge3/envs/sowhat/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/sowhat.t .. 1/2 # 
# Now running a SOWH test. This usually takes less than a minute...
Can't exec "raxmlHPC": Datei oder Verzeichnis nicht gefunden at sowhat line 394.
Use of uninitialized value $version_st in split at sowhat line 395.
Error from RAxML (check --rax option):
t/sowhat.t .. 2/2 
#   Failed test 'was able to run example 1'
#   at t/sowhat.t line 17.
#          got: '512'
#     expected: '0'
# Looks like you failed 1 test of 2.
t/sowhat.t .. Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/2 subtests 

Test Summary Report
-------------------
t/sowhat.t (Wstat: 256 Tests: 2 Failed: 1)
  Failed test:  2
  Non-zero exit status: 1
Files=1, Tests=2,  2 wallclock secs ( 0.04 usr  0.01 sys +  0.89 cusr  0.18 csys =  1.12 CPU)
Result: FAIL
Failed 1/1 test programs. 1/2 subtests failed.
make: *** [test_dynamic] Fehler 1

Cheers Bastian

[josephryan]

Try:

# if not already activated
conda activate /home/uni08/bheimbu/miniforge3/envs/sowhat

# install prerequisite
conda install -c bioconda raxml

[bheimbu]

The second line did the trick, the environment was activated before actually.

Thanks for your help,

Cheers Bastian

[bheimbu]

Anyway,

now my question would be, how to compare two trees with each other, reconstructed with IQ-Tree (so there would be no need to use RAxML here). Is this possible with sowhat. Something like this…

# TEST14: Datatype = DNA, Model = GTRGAMMA, ML Software = RAxML, compare two trees, neither of which is the most likely topology (not a typical SOWH test)
sowhat --constraint=examples/H0.tre --aln=examples/nt.phy --raxml_model=GTRGAMMA --dir=test.output/test15 --name=test --treetwo=examples/H1.tre --json

…but without the RAxML stuff, right?

[josephryan]

To run the SOWH test you need to generate trees. sowhat uses raxml (which is roughly equivalent to iqtree). We hope to make the program work with iqtree at some point.

I think you want to run 2 sowh tests and compare the p-values. Reading the sowhat paper should help understand exactly how the SOWH test is working. https://academic.oup.com/sysbio/article/64/6/1048/1669595

Good luck

[bheimbu]

Just to clarify a few things: sowhat always uses a constraint tree to run, right? But I want to check whether my unconstrained tree is better than my constrained tree (hypothetical tree based on supposed family relationships between mites)? To be honest, I know that the unconstrained tree is better, because some supposed family relationships are non-sense. Maybe, sowhat is not the right software to test this?

Cheers Bastian