Open vinitamehlawat opened 2 years ago
Dear Vinita,
unfortunately, our mptp expert has left academia. Do you really need to run species tree delimitation (that's what mptp does) or can you skip this part? If you really need it we'll try to help you, but I prefer asking before "wasting" time ;-)
Benoit
Hi @BenoitMorel
My aim for using your pipeline to get phylogentic tree for my SARS-data with a very good boot support value(BS), If you think 9_mptp_on_all_trees.py
script is not impacting my factor then I can skip this.
Thank you Vinita
That's good news :-) The mptp step is irrelevant for the tree and the support values. The rooting steps that are also causing you trouble are also irrelevant for you (rootdigger and epa).
Getting good support values for all branches will be difficult, but maybe you can get good values for some important branches... In our study, we tried running tree thinning (removing lots of the input sequences to keep to ones that we expect to have a strong phylogenetic signal). If you are ok with discarding sequences, that might be a good option for you. But As far as I remember, we also didn't get good support after thinning.
I am not sure that tree thinning is well documented and that the current script does exactly what's described in my paper. I will check it and keep you in touch today.
Best, Benoit
Hi @Pbdas
I ran
./pipeline/9_mptp_on_all_trees.py work_dir/2021-11-19_00/fmsan/
and I got following error on my terminalWARNING: delimit was not compiled with libgsl. Likelihood ratio test disabled. WARNING: A speciation edge is smaller than the specified minimum branch length. mptp 0.2.4_linux_x86_64, 1008GB RAM, 96 cores https://github.com/Pas-Kapli/mptp WARNING: delimit was not compiled with libgsl. Likelihood ratio test disabled. WARNING: A speciation edge is smaller than the specified minimum branch length. WARNING: delimit was not compiled with libgsl. Likelihood ratio test disabled. Traceback (most recent call last): File "/home/vinita/covid19_cme_analysis/./pipeline/9_mptp_on_all_trees.py", line 191, in
run_mptp_all_rootings_on_trees_one_histogram(paths.raxml_credible_ml_trees, paths.mptp_output, paths.mptp_output_summary_all_rootings_one_histogram)
File "/home/vinita/covid19_cme_analysis/./pipeline/9_mptp_on_all_trees.py", line 181, in run_mptp_all_rootings_on_trees_one_histogram
species = get_all_rootings_counts_one_histogram(results_all_rootings_ml + "/output.txt", species)
File "/home/vinita/covid19_cme_analysis/./pipeline/9_mptp_on_all_trees.py", line 105, in get_all_rootings_counts_one_histogram
for i in range(4, len(lines)):
TypeError: object of type '_io.TextIOWrapper' has no len()
I also found so many
tempOutFooBar_.svg
something around 3000 in number , Please have a look at this error .