josephryan / sowhat Goto Github PK

Stopping criterion would be met after a minimum number of samples (say 100) and when the p-value and the confidence interval fall entirely on the same side of the significance level.

The error that currently is output is a confusing message from RAxML.

Only simple partitioning schemes are currently allowed.
Improve feature to allow partitioning schemes that cover multiple non-contiguous regions of an alignment, that are listed out of order, or that divide by codon position.

"The problem with these arguments is that you have set the maximum number of reps to 2 (--reps=2) - this means that sowhat will generate only two simulated datasets and this is not enough to calculate any statistics, such as a p-value. sowhat won't start printing a sowhat.results.txt file until after the 10th bootstrap replicate to avoid choking on any mathematical errors near the start of the analysis. We strongly recommend each analysis should use 100+ bootstrap replicates, and that the number of bootstraps (the sample size) should be justified by reporting the confidence interval surrounding the p-value"

Bootstrapping the package in and using that to cpan R

My fix was to remove the command-line switch from the system call to R in 'Statistics/R/Bridge/Linux.pm'. We need to at least warn users. Probably should write the author(s) of Statistics::R. Not sure if this affects other versions.

this needs to be a system independent method using Perl module

perhaps also seq-gen version.

the _structure_subroutine needs to be edited so that the report is corrected, by switching the ml and t1 values.

RAxML v 8.1.20

Currently only the version of RAxML is recorded. It would be helpful to have the following versions recorded in the results:

1. sowhat version
2. seq-gen version
3. PhyloBayes version (if used)
4. Garli version (if used)

current warning is that taxa dont match up, difficult to sort out.

This message "Constraint_X is more likely than Y, X will be used as the constraint tree instead" is only printed to STDERR. This information should also go in the results file. In general there should be more details about which tree is which in the results file.

Need to add a description of sample datasets to README.md. These should explain the origins of the datasets, as well as list some basic attributes (number of taxa, number of genes, number of sites). There should also be an indication of which files pertain to which datasets.

The TravisCI test is failing: https://travis-ci.org/josephryan/sowhat/builds/221453597

The problem seems to be:

• The test images is based on Ubuntu 14.04.5 LTS
• sudo apt-get install -y r-base installs R 3.0.2
• The ape package is unavailable for this older R, throwing the warning package 'ape' is not available (for R version 3.0.2)
• Results in the error library(ape) : there is no package called 'ape'

We should figure out how to install a more recent version of R on this container or use a different test image that allows installation of newer R.

Right now limited to most likely topology vs. a single alternative.

clean up and reprioritize documentation.

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

run an initial tree with AUTO specified and then after parsing the info file, use the determined best model for all downstream analyses.

Will require running seq-gen in aminoacid mode and up to 20 substitutions. multistate currently fails with: "expecting 2 frequencies. Multi-State only works w/binary matrix".

Self evident.

see: http://search.cpan.org/~oliver/Test-Subroutines-1.113350/lib/Test/Subroutines.pm

This is a known issue, and is addressed here:

https://groups.google.com/forum/#!topic/raxml/qn7_ZXoJTHg

We should redo some of hte problematic searches with the addition of the --no-bfgs raxml option. If that fixes the problem for those matrices, we should rerun the tests in the manuscript that were impacted by this. If they work, we should revise the manuscript to reflect the fix.

SOWH tests can take a long time on large datasets. Here are some ideas on how to monitor a job and how to cut a job short. These should be considered (and tested) for being added to the documentation:

1. Monitoring a job
   the following command can be used to monitor a job (only if reps = 1 - the default) if run from within the directory that was specified with the --dir option:

   ls -1 sowhat_scratch/ | cut -f 4 -d '.' | sort -n | tail -n1

2. Cutting a job short
   If the job is currently running, make a copy of the directory that was specified with the --dir option (and its contents) :

   cp -R myoutputdir rerunoutputdir

   run the exact same command as before, but with this new directory as the --dir option, and

   --reps=SMALLER_NUMBER_OF_REPS --restart

At present the output is simple text. This makes it difficult for it to be machine readable since text format may change in unspecified ways from version to version, and therefor for SOWHAT to be wrapped into larger workflows.

We should generate structured output as a json file. This should then be read and formatted as a text output, similar to what we have now. It could also be parsed into an easy-to-read html output.

This does not seem to be installed by default with Perl.

IQtree may offer advantages to RAxML, GARLi. SOWHAT will need to read the required output from the results files (base freqs, transition rates, likelihood).

Add testing via travis-ci. Dependencies can be installed as described at https://docs.travis-ci.com/user/installing-dependencies/

eg

#cycle #treegen time loglik length alpha nmode stat
1 940 2836 -889000 21.9549 0.585788 4885 0.933128