poonlab/comet-prot

Book chapter for upcoming Springer book Computational Methods in Protein Evolution

comet-prot's Issues

Use Springer LaTeX template

https://www.springer.com/gp/authors-editors/book-authors-editors/manuscript-preparation/5636

bayesgraph not working

After I got my nice ancestral reconstruction CSV file I ran:

HYPHYMPI BASEPATH=/usr/local/lib/hyphy /home/marianoavino/Desktop/HCV/scripts/bayesgraph.bf

and I got this error message:

Error:

Master node received an error:Could not read command file in ExecuteAFile.
Original path: 'bayesgraph.ibf.txt'.
Expanded path: '/home/marianoavino/Desktop/HCV/scripts/bayesgraph.ibf.txt'

Function call stack
1 : ExecuteAFile from file "bayesgraph.ibf.txt" using basepath /home/marianoavino/Desktop/HCV/scripts/.
-------
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD 
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.

@ArtPoon

Explain autocorrelation

Figure 1 legend

The choice of a phylogenetic tree for the analysis

Re-reading the paper I came across this sentence:
"To run this analysis, you need to have a codon sequence alignment and a phylogenetic tree relating these sequences" at line 173
and then at line 189 "A phylogenetic tree can be reconstructed from the sequence alignment using any standard maximum likelihood program such as RAxML \cite{Stamatakis:2014} (\url{https://github.com/stamatak/standard-RAxML}) or PhyML \cite{Guindon:2010}" .
It looks to me here that we are granting that a phylogenetic tree is always a maximum likelihood phylogenetic tree, while there are other phylogenetic trees that can be made (MP, for example). Shall we say a word here that we do prefer maximum likelihood phylogenetic trees for certain reasons?

Missing reference for H77

Clean up repo

There are a bunch of extra data files and scripts that we didn't end up using for the book chapter.
We also need to write a README.md

The fig:tree was not cited in the text

The fig:tree was not cited in the text

Formatting requests

• key words
• running head
• double spacing
• references numbered in order of appearance
• separate all subheadings from associated text (line break)
• figures in separate files from main text
• notes is section 4, do not number acknowledgements section

Segmentation problem

After I run the command:

HYPHYMPI BASEPATH=/usr/local/lib/hyphy /home/marianoavino/Desktop/HCV/scripts/bayesgraph.bf

I get this problem:

Read 1180 cases from file.
Detected 195 variables.
Reduced data to 67 sites
[Rei:22257] *** Process received signal ***
[Rei:22257] Signal: Segmentation fault (11)
[Rei:22257] Signal code: Address not mapped (1)
[Rei:22257] Failing at address: 0x3c2236501
[Rei:22257] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x11390)[0x7f62c3e39390]
[Rei:22257] [ 1] HYPHYMPI(_ZN7_Matrix4HashEll+0x5a)[0x5a2a5a]
[Rei:22257] [ 2] HYPHYMPI(_ZN7_MatrixclEll+0x6)[0x5a6f76]
[Rei:22257] [ 3] HYPHYMPI(_ZN23_BayesianGraphicalModel7ComputeER11_SimpleListP5_List+0x1a8)[0x5e3ba8]
[Rei:22257] [ 4] HYPHYMPI(_ZN23_BayesianGraphicalModel15OrderMetropolisEblldP7_Matrix+0x292)[0x5e9fb2]
[Rei:22257] [ 5] HYPHYMPI(_ZN23_BayesianGraphicalModel8OptimizeEv+0x474)[0x5edb94]
[Rei:22257] [ 6] HYPHYMPI(_ZN18_ElementaryCommand30HandleOptimizeCovarianceMatrixER14_ExecutionListb+0x1ae)[0x52926e]
[Rei:22257] [ 7] HYPHYMPI(_ZN18_ElementaryCommand7ExecuteER14_ExecutionList+0xd05)[0x493085]
[Rei:22257] [ 8] HYPHYMPI(_ZN14_ExecutionList7ExecuteEv+0x23d)[0x493ffd]
[Rei:22257] [ 9] HYPHYMPI(_ZN18_ElementaryCommand13ExecuteCase39ER14_ExecutionList+0x4cd)[0x49480d]
[Rei:22257] [10] HYPHYMPI(_ZN18_ElementaryCommand7ExecuteER14_ExecutionList+0xeb3)[0x493233]
[Rei:22257] [11] HYPHYMPI(_ZN14_ExecutionList7ExecuteEv+0x23d)[0x493ffd]
[Rei:22257] [12] HYPHYMPI(_ZN10_Operation7ExecuteER6_StackP18_VariableContainerP7_String+0xe94)[0x457774]
[Rei:22257] [13] HYPHYMPI(_ZN8_Formula7ComputeElP18_VariableContainerP5_ListP7_String+0x90)[0x499a10]
[Rei:22257] [14] HYPHYMPI(_Z14ExecuteFormulaP8_FormulaS0_llP18_VariableContainerc+0x114)[0x596094]
[Rei:22257] [15] HYPHYMPI(_ZN18_ElementaryCommand12ExecuteCase0ER14_ExecutionList+0x287)[0x48e7b7]
[Rei:22257] [16] HYPHYMPI(_ZN18_ElementaryCommand7ExecuteER14_ExecutionList+0x6bb)[0x492a3b]
[Rei:22257] [17] HYPHYMPI(_ZN14_ExecutionList7ExecuteEv+0x23d)[0x493ffd]
[Rei:22257] [18] HYPHYMPI(main+0xc35)[0x441f05]
[Rei:22257] [19] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7f62c2cec830]
[Rei:22257] [20] HYPHYMPI(_start+0x29)[0x442959]
[Rei:22257] *** End of error message ***
Segmentation fault (core dumped)

Modify bayesgraph to generate labels and incorporate them into outputs

bayesgraph.bf issues

When I leave the header on I get the following (includes command line):

HYPHYMPI BASEPATH=/usr/local/lib/hyphy /home/marianoavino/Desktop/HCV/scripts/bayesgraph.bf

/home/marianoavino/Desktop/HCV/scripts/Select file containing substitution matrix in CSV format:/home/marianoavino/Desktop/HCV/N55b/ancestral.csv
Does this file contain a header row? (Y\n)Y
Read 1069 cases from file.
Detected 592 variables.
Enter minimum number of substitutions per site (1-135): 2
Reduced data to 231 sites
Maximum number of parents per node (default 1):2
Length of burn-in (default 10000): 
Length of chain post-burn-in (default 100000): 
Number of samples (default 100): 

/home/marianoavino/Desktop/HCV/scripts/Provide a file to write edge posterior outputs:/home/marianoavino/Desktop/HCV/N55b/chain1
[Rei:18464] *** Process received signal ***
[Rei:18464] Signal: Segmentation fault (11)
[Rei:18464] Signal code: Address not mapped (1)
[Rei:18464] Failing at address: 0x965b840
[Rei:18464] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x11390)[0x7fc1e8e52390]
[Rei:18464] [ 1] HYPHYMPI(_ZN7_Matrix4HashEll+0x5a)[0x5a2a5a]
[Rei:18464] [ 2] HYPHYMPI(_ZN7_MatrixclEll+0x6)[0x5a6f76]
[Rei:18464] [ 3] HYPHYMPI(_ZN23_BayesianGraphicalModel7ComputeER11_SimpleListP5_List+0x1a8)[0x5e3ba8]
[Rei:18464] [ 4] HYPHYMPI(_ZN23_BayesianGraphicalModel15OrderMetropolisEblldP7_Matrix+0x292)[0x5e9fb2]
[Rei:18464] [ 5] HYPHYMPI(_ZN23_BayesianGraphicalModel8OptimizeEv+0x474)[0x5edb94]
[Rei:18464] [ 6] HYPHYMPI(_ZN18_ElementaryCommand30HandleOptimizeCovarianceMatrixER14_ExecutionListb+0x1ae)[0x52926e]
[Rei:18464] [ 7] HYPHYMPI(_ZN18_ElementaryCommand7ExecuteER14_ExecutionList+0xd05)[0x493085]
[Rei:18464] [ 8] HYPHYMPI(_ZN14_ExecutionList7ExecuteEv+0x23d)[0x493ffd]
[Rei:18464] [ 9] HYPHYMPI(_ZN18_ElementaryCommand13ExecuteCase39ER14_ExecutionList+0x4cd)[0x49480d]
[Rei:18464] [10] HYPHYMPI(_ZN18_ElementaryCommand7ExecuteER14_ExecutionList+0xeb3)[0x493233]
[Rei:18464] [11] HYPHYMPI(_ZN14_ExecutionList7ExecuteEv+0x23d)[0x493ffd]
[Rei:18464] [12] HYPHYMPI(_ZN10_Operation7ExecuteER6_StackP18_VariableContainerP7_String+0xe94)[0x457774]
[Rei:18464] [13] HYPHYMPI(_ZN8_Formula7ComputeElP18_VariableContainerP5_ListP7_String+0x90)[0x499a10]
[Rei:18464] [14] HYPHYMPI(_Z14ExecuteFormulaP8_FormulaS0_llP18_VariableContainerc+0x114)[0x596094]
[Rei:18464] [15] HYPHYMPI(_ZN18_ElementaryCommand12ExecuteCase0ER14_ExecutionList+0x287)[0x48e7b7]
[Rei:18464] [16] HYPHYMPI(_ZN18_ElementaryCommand7ExecuteER14_ExecutionList+0x6bb)[0x492a3b]
[Rei:18464] [17] HYPHYMPI(_ZN14_ExecutionList7ExecuteEv+0x23d)[0x493ffd]
[Rei:18464] [18] HYPHYMPI(main+0xc35)[0x441f05]
[Rei:18464] [19] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7fc1e7d05830]
[Rei:18464] [20] HYPHYMPI(_start+0x29)[0x442959]
[Rei:18464] *** End of error message ***
Segmentation fault (core dumped)

When I do not have a header file:

HYPHYMPI BASEPATH=/usr/local/lib/hyphy /home/marianoavino/Desktop/HCV/scripts/bayesgraph.bf

/home/marianoavino/Desktop/HCV/scripts/Select file containing substitution matrix in CSV format:/home/marianoavino/Desktop/HCV/N55b/ancestralnoheader.csv
Does this file contain a header row? (Y\n)n
Read 1069 cases from file.
Detected 592 variables.
Enter minimum number of substitutions per site (1-135): 2
Reduced data to 231 sites
Maximum number of parents per node (default 1):2
Length of burn-in (default 10000): 
Length of chain post-burn-in (default 100000): 
Number of samples (default 100): 

/home/marianoavino/Desktop/HCV/scripts/Provide a file to write edge posterior outputs:/home/marianoavino/Desktop/HCV/N55b/chain1
Error:

Master node received an error:Invalid node name (expected a string) passed to a BGM constructor

Function call stack
1 : BayesianGraphicalModel my_bgm=(nodes)
-------
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD 
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.

Look into making inset figure for Figure 2