Installation problem: SCORE_MAT_PATH

[VincentBoivin]

Whenever I launch MstatX I keep having the same error message: "Cannot open file data/aaindex/HENS920102.mat"

Setting the $SCORE_MAT_PATH variable in my .bashrc to /path/to/mstatX/ , /path/to/mstatX/data/ or /path/to/mstatX/data/aaindex doesn't change a thing. I keep getting the same error message.

When I try to go around this issue by specifying the -m option like this: -m /path/to/mstatX/data/aaindex/HENS920102.mat gives this error instead: "Error: type list is empty"

Any clue as to how I can make it work?

[gcollet]

I corrected the problem with SCORE_MAT_PATH. The message "Error: type list is empty" is because Mstatx cannot find any amino acid in a given column. I changed the message so you can see on which column it appears.

Tell me if it solves your problem.

[Ptero64]

Hello, I think I have the same issue despite using the last version of the script. I try to run MstatX as part of the pipeline HybPhyloMaker. When I want to run mstatx I get the message: Error: Environment variable SCORE_MAT_PATH is needed

I had the path to ~/MstatX/ ; ~/MstatX/data/; and ~/MstatX/data/aaindex or using option -m (same as -sp indicated in pdf?) to DNA.mat for example.

Do you have idea how to fix it?

Thanks in advance

[gcollet]

Hi. Can you give me an example ? A command line you use when you get the message ?

[gcollet]

The -sp flag is deprecated, only use -m flag to give a specific matrix. I removed it from the manual.

[Ptero64]

Hi, Part of the pipeline the line is: mstatx -i $file -g > /dev/null line=$(cat output.txt) echo -e "$file\t$line" >> mstatx.txt done the message is:

[Ptero64]

Calculating alignment entropy for all genes using MstatX... CorrectedAssembly_1.fasta Error: Environment variable SCORE_MAT_PATH is needed

Usage: mstatx [options]

Available statistics: sumofpairs (1) wentropy (1) trident (1) mvector (1) jensen (1) kabat (1) gap (1)

Options:

cat: output.txt: No such file or directory rm: cannot remove 'output.txt': No such file or directory

[Ptero64]

I tried also to run it alone after install it on the server. I try those command: mstatx -i test.fas -g -o test.txt mstatx -i test.fas -m /path/MstatX/data/DNA.mat -g > test.txt get this message

[Ptero64]

Error: Environment variable SCORE_MAT_PATH is needed Usage: mstatx [options]

Available statistics: sumofpairs (1) wentropy (1) trident (1) mvector (1) jensen (1) kabat (1) gap (1)

Options:

[gcollet]

I use the function getenv to get the environment variable... Are you sure the SCORE_MAT_PATH is set ?

Nevertheless, I made some changes so that you don't get an error when using -m option.

Can you pull and tell me if this new version corrects your error ?

[Ptero64]

Hi, Thanks for your answer. I don't know how work getenv. I had the path the folder data & aaindex. run also make and get this: g++ -O3 -Wall -lm -lpthread -o mstatx src/*.cpp src/trident.cpp: In member function ‘virtual void TridStat::calculate(Msa&)’: src/trident.cpp:164:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (type_list.find("-") < (int) type_list.size()){

I have retry but not sure it has worked as intended, but got an ouptut this time. Still not find the PATH. btx246@frontend11:~/MstatX$ mstatx -i A3GALT2_MAFFT_aln_Without_low_SP_col.fas -g -o test.txt -m /data2/home/btx246/MstatX/data/DNA.mat Warning: Environment variable SCORE_MAT_PATH is not found SCORE_MAT_PATH is not set, use data/aaindex instead Statistic: wentropy

Multiple alignment : nb seq = 10, nb col = 879 Mstatx computed in 0 seconds Results are written in test.txt

[pespindola]

Hi, I'm running the program with default parameters without errors, like this:

mstatx -i $f -g -o TemporalResult.txt > /dev/null

The output looks like: Seq wentropy 2_0_test.fa 0.132202 2_1_identical.fa 3.0097e-07 2_2_50identical.fa 0.293112 1_example_valdar.mali 0.400176

but now I'm having a hard time trying to interpret the results. Could you give some guidelines, please?

I made this set of sequences to test. The original valdar.mali and the others are short sequences, where 2_1_identical.fa has no variation at all, 2_2_50identical.fa has a variation on half of the sequence, and the other is random.

can I use default parameters with DNA ?? or should I change the matrix ?? Are there some possible meaningful thresholds??

Thanks!

[chenwx-up]

Hi, when I run make to install, an error has appear: In file included from src/jensen.cpp:24: src/scoring_matrix.h:47:29: error: redefinition of ‘char aa’ 47 | float score(char aa, char aa); | ~~~~~^~ src/scoring_matrix.h:47:20: note: ‘char aa’ previously declared here 47 | float score(char aa, char aa); | ~~~~~^~ src/scoring_matrix.h:48:33: error: redefinition of ‘char aa’ 48 | float normScore(char aa, char aa); | ~~~~~^~ src/scoring_matrix.h:48:24: note: ‘char aa’ previously declared here 48 | float normScore(char aa, char aa);

Colud you please tell me how to do ?

Best, Chen