xavierdidelot / clonalframeml Goto Github PK

Dear Xavier/Daniel,
I want to estimates of recombinations and mutations occurring in each strain. I followed your user guide and got the results. I got R/theta, 1/delta, nu and M for each strain and node. For strain 1, r/m=R/theta× delta×nu=0.0535089×(1/2.20429)×5.99138, is that right? Why the delta is so small?
Would you please help me about this? Waiting for your help. Thank you very much.
Parameter Branch Posterior Mean Posterior Variance a_post b_post
R/theta Mean 1.30403 NA NA NA
1/delta Mean 0.00838315 NA NA NA
nu Mean 0.0410816 NA NA NA
M Mean 0.00358976 NA NA NA
R/theta 1 0.0535089 3.07841e-05 93.0091 1738.2
1/delta 1 2.20429 0.0522412 93.0091 42.1945
nu 1 5.99138 0.035712 1005.17 167.769
M 1 0.255673 4.92296e-05 1327.83 5193.48
R/theta 2 3.0759 0.00175824 5381.04 1749.42
1/delta 2 0.552766 5.67901e-05 5380.34 9733.49
nu 2 3.27466 6.87087e-05 156070 47660
M 2 1.29058 0.00123671 1346.78 1043.55

Best wishes,
vivienne

Your tutorial link to XFMA is broken:

http://asap.ahabs.wisc.edu/mauve-aligner/mauve-user-guide/mauve-output-file-form
ats.html

Maybe Aaron's new lab page is a good replacement:

http://darlinglab.org/mauve/user-guide/files.html

Original issue reported on code.google.com by [email protected] on 17 Feb 2015 at 3:21

Hello,

I am trying to use clonalframeML but I encountered an error.
"Read 47 sequences of length 14399 sites from Giardia_allB.fasta
ERROR: convert_NewickTree_to_marginal_tree(): Number of descendant nodes (4) incompatible with a strictly bifurcating rooted tree"

What does it mean? Any advice. I appreciate this. Thanks,

Hi

Just wondering if there is any documentation available, or if you could explain 
what the color scheme represents in the pdf that is generated with the 
cfml_results.R script.

As far as I can gather, light blue represents all invariant sites, white all 
variant sites and dark blue the regions deemed recombinant (please correct if 
this is wrong). However, I am not sure about the yellows, oranges and reds. 
(pdf attached)

Any help would be greatly appreciated.

Sarah

Original issue reported on code.google.com by [email protected] on 24 Apr 2015 at 5:19

Attachments:

• example.pdf

Dear Xavier,

I am experiencing an issue that apparently is closely related to two athers reported previously (#7, #17), but the solution does not seem to apply to my situation.

I am trying to perform a recombination analysis on 6 bacterial genomes. The two input files provided to the software are an xmfa alignment and a guide tree in Newick format, both constructed with MAUVE.

I run the command:
./ClonalFrameML /home/prova1.nwk /home/prova1.xmfa /home/prova1_out -xmfa_file true -show_progress true

but I get the following error:

"ClonalFrameML version 1.-178
xmfa_file = true
show_progress = true
Finished reading in control file.

Read 6 sequences of length 2844495 sites from /home/prova1.xmfa
ERROR: convert_NewickTree_to_marginal_tree(): Newick tree tip label seq5 was not expected"

I have tried to edit the Newick file to change or remove tip labels, but that did not change the situation.

Could you please help me to resolve this?

All the best

Ed

P.S. sorry for the double post, but I have just noticed that the original one was posted by mistake as a reply to the closed Issue #17.

To visualize (create the pdf) the results I need to execute this line:
Rscript cfml_results.R output_prefix

I downloaded the source "ClonalFrame v1.8 Source Code.zip" and used the make 
file to compile ClonalFrame. But I can not find the R-Script in any of the 
provided folders.

Maybe it should have been generated as part of the output files?

Original issue reported on code.google.com by [email protected] on 3 Mar 2015 at 9:18

While using XMFA file I get message: "Segmentation fault: 11".

./ClonalFrameML mauve.guide_tree mauve_align mauve_out -xmfa_file true
ClonalFrameML v1.0-19-g9488a80
xmfa_file = true
Finished reading in control file.

Read 24 sequences of length 6594565 sites from mauve_align
Segmentation fault: 11

What does it mean?

Thanks in advance!

Hi when I try to compile the latest src I get the following error. Please could you advise on if this is an environment issue or code bug?

Many thanks

In file included from ./coalesce/coalesce.h:22,
                 from ./main.h:24,
                 from main.cpp:20:
./coalesce/coalescent_control.h: In member function ‘Control& Control::read_input(char*)’:
./coalesce/coalescent_control.h:121: warning: deprecated conversion from string constant to ‘char*’
./coalesce/coalescent_control.h:124: warning: deprecated conversion from string constant to ‘char*’
./coalesce/coalescent_control.h:128: warning: deprecated conversion from string constant to ‘char*’
./coalesce/coalescent_control.h:135: warning: deprecated conversion from string constant to ‘char*’
./coalesce/coalescent_control.h:136: warning: deprecated conversion from string constant to ‘char*’
./coalesce/coalescent_control.h:144: warning: deprecated conversion from string constant to ‘char*’
./coalesce/coalescent_control.h:159: warning: deprecated conversion from string constant to ‘char*’
./coalesce/coalescent_control.h:162: warning: deprecated conversion from string constant to ‘char*’
./coalesce/coalescent_control.h:170: warning: deprecated conversion from string constant to ‘char*’
./coalesce/coalescent_control.h: In member function ‘Control& Control::vector_to_Matrix(std::vector<double, std::allocator<double> >*, myutils::Matrix<double>*, int, int)’:
./coalesce/coalescent_control.h:202: warning: deprecated conversion from string constant to ‘char*’
./coalesce/coalescent_control.h:203: warning: deprecated conversion from string constant to ‘char*’
./coalesce/coalescent_control.h: In member function ‘Control& Control::read_mut_matrix(myutils::Matrix<double>&, std::vector<double, std::allocator<double> >&)’:
./coalesce/coalescent_control.h:224: warning: deprecated conversion from string constant to ‘char*’
./coalesce/coalescent_control.h:231: warning: deprecated conversion from string constant to ‘char*’
./coalesce/coalescent_control.h:234: warning: deprecated conversion from string constant to ‘char*’
./coalesce/coalescent_control.h:239: warning: deprecated conversion from string constant to ‘char*’
./coalesce/coalescent_control.h:243: warning: deprecated conversion from string constant to ‘char*’
./coalesce/coalescent_control.h:246: warning: deprecated conversion from string constant to ‘char*’
In file included from ./coalesce/coalescent_process.h:35,
                 from ./coalesce/coalesce.h:23,
                 from ./main.h:24,
                 from main.cpp:20:
./coalesce/coalescent_record.h: In member function ‘mt_node* marginal_tree::coalesce(double&, int&, int&)’:
./coalesce/coalescent_record.h:119: warning: deprecated conversion from string constant to ‘char*’
./coalesce/coalescent_record.h:126: warning: deprecated conversion from string constant to ‘char*’
./coalesce/coalescent_record.h: In member function ‘mt_node* marginal_tree::migrate_coalesce(double&, int&, int&)’:
./coalesce/coalescent_record.h:148: warning: deprecated conversion from string constant to ‘char*’
./coalesce/coalescent_record.h:155: warning: deprecated conversion from string constant to ‘char*’
main.cpp: In function ‘void write_importation_status_intervals(std::vector<std::vector<ImportationState, std::allocator<ImportationState> >, std::allocator<std::vector<ImportationState, std::allocator<ImportationState> > > >&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&, std::vector<bool, std::allocator<bool> >&, std::vector<int, std::allocator<int> >&, std::ofstream&, int, const char*)’:
main.cpp:1892: error: ‘strlen’ was not declared in this scope
main.cpp:1903: error: ‘strlen’ was not declared in this scope
main.cpp:1916: error: ‘strlen’ was not declared in this scope

Salut Xavier,

I manage to perform dataviz of the ClonalFrameML analysis. Unfortunatly, I didn't manage to find the legend of the produced figure and the way to interpret it.

I also have a problem with the legend when there's too much isolates. I tried to change the line

axis(1); axis(2,1:nrow(wh.mut),ifelse((1:nrow(wh.mut))<=ceiling(nrow(wh.mut)/2),rownames(wh.mut),"")[od],las=2,cex.axis=.4); box()

axis(1); axis(2,1:nrow(wh.mut),ifelse((1:nrow(wh.mut))<=ceiling(nrow(wh.mut)/2),rownames(wh.mut),"")[od],las=2,cex.axis=.2); box()

It's better but not perfect (example figure). Any idea to solve this misqtke?

Best regards

Can this output be in proper BED format? It would be really useful to use in othertools as well.

I think the only thing missing is chr value to be the first column, instead of sample/internal branch.

So instead of:

    Node       Beginning      End
    NODE_12    12              1234
    SAMPLE1    1235            1245

We get

    chr    12                 1234    NODE_12
    chr    1235               1245    SAMPLE1

Perhaps the same of the chr can be supplied to the command line?

Dear Xavier/Daniel,

As for the per-branch model, the default value of parameter "-embranch_dispersion" is 0.01, and it was set to 0.1 in the example of S. aureus. I read your paper and can't find any description about it. So could you please explain the meaning of this parameter and how would it influence the result?

Best regards!
xiaohai

Dear Xavier,
I am running into some problems while running ClonalFrameML. I used as input an alignment in the standard fasta format. I used this file to create a tree using RaxML in Galaxy. I then run the software as
$ /Software/clonalframeml-read-only/src/ClonalFrameML CF170_RaxML-Chr3.nwk CF170_orderedSNPAlignment_Chr3.fa chr3.output > chr3.log.txt

alignmentInFasta.txt
RaxML_Newick.txt

However, I run into the following error:

ClonalFrameML version 1.-178
Finished reading in control file.

Read 111 sequences of length 177 sites from CF170_orderedSNPAlignment_Chr3.fa
ERROR: convert_NewickTree_to_marginal_tree(): Newick tree tip label 2 was not expected

I was not expecting this error since I created the tree with the same fasta I'm using for ClonalFrameML. I saw that in a previous post you suggested removing the bootstrap values, which I tried but that does not seem to be the problem. Could you please help me with this problem?

I have an additional question. This dataset includes only the polymorphic sties from the entire genomes of intraclonal bacteria (meaning I don't expect any genomic rearrangements amongst these genomes). Is this data appropriate as input for CFML? I am just wondering about this since the relative distance between the polymorphic sites are not input.

Thanks in advance for your time.
Julio Diaz Caballero

Dear Dr. Didelot,

I have tried to compile the version 1.2 of ClonalFrame in a Linux server with RedHat 7.1
My gcc version is 4.8.3.

After the qmake;make; the output was:

g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/lib64/qt4/mkspecs/linux-g++ -I. -I/usr/include/QtCore -I/usr/include/QtGui -I/usr/include -Ibuild -o build/alignment_xmfa.o src/alignment_xmfa.cpp
src/alignment_xmfa.cpp: In constructor ‘wb::Alignment_xmfa::Alignment_xmfa(char*, bool, int)’:
src/alignment_xmfa.cpp:61:125: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘std::vector<int>::size_type {aka long unsigned int}’ [-Wformat=]
                     printf("Warning: ignoring incomplete fragment %d (does not contain strain %s)\n",v.size(),names[missing]);
                                                                                                                             ^
src/alignment_xmfa.cpp:129:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     for (j=0;j<strlen(bufin[i]);j++) {
                                               ^
src/alignment_xmfa.cpp: In member function ‘void wb::Alignment_xmfa::Fgets(char*, int, FILE*)’:
src/alignment_xmfa.cpp:187:23: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
         fgets(buf,l,f);
                       ^
src/alignment_xmfa.cpp:189:27: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
             fgets(buf,l,f);
                           ^
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/lib64/qt4/mkspecs/linux-g++ -I. -I/usr/include/QtCore -I/usr/include/QtGui -I/usr/include -Ibuild -o build/alignment_structure.o src/alignment_structure.cpp
src/alignment_structure.cpp: In constructor ‘wb::Alignment_structure::Alignment_structure(char*, int)’:
src/alignment_structure.cpp:45:19: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
             if (ch>='0' & ch<='9')
                   ^
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/lib64/qt4/mkspecs/linux-g++ -I. -I/usr/include/QtCore -I/usr/include/QtGui -I/usr/include -Ibuild -o build/alignment.o src/alignment.cpp
src/alignment.cpp: In member function ‘void wb::Alignment::writeToFile(char*)’:
src/alignment.cpp:236:21: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
         char * lets="ATCG";
                     ^
src/alignment.cpp:241:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (unsigned int i=0;i<getB();i++) {
                                      ^
src/alignment.cpp:243:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (unsigned int j=0;j<getN();j++) {
                                          ^
src/alignment.cpp:244:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (unsigned int k=beg;k<end;k++)
                                           ^
src/alignment.cpp:246:41: warning: embedded ‘\0’ in format [-Wformat-contains-nul]
                 sprintf(buf+end-beg,"\0");
                                         ^
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/lib64/qt4/mkspecs/linux-g++ -I. -I/usr/include/QtCore -I/usr/include/QtGui -I/usr/include -Ibuild -o build/boot.o src/boot.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/lib64/qt4/mkspecs/linux-g++ -I. -I/usr/include/QtCore -I/usr/include/QtGui -I/usr/include -Ibuild -o build/burst.o src/burst.cpp
src/burst.cpp: In member function ‘void wb::Burst::burst(wb::Param*)’:
src/burst.cpp:170:47: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘std::vector<std::vector<int> >::size_type {aka long unsigned int}’ [-Wformat=]
         printf("Nb groups=%d\n",groups->size());
                                               ^
src/burst.cpp:188:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     for (k=1;k<rid->size();k++)
                                          ^
src/burst.cpp:190:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (k>=rid->size()) continue;
                                      ^
src/burst.cpp: In member function ‘void wb::Burst::optimiseFathers(gsl_vector_int*, std::vector<std::vector<int> >*, int)’:
src/burst.cpp:259:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 if (slvs->at(prop).size()>current && !descended(prop,i,fathers)) {
                                           ^
src/burst.cpp: At global scope:
src/burst.cpp:252:10: warning: unused parameter ‘f’ [-Wunused-parameter]
     void Burst::optimiseFathers(gsl_vector_int * fathers,vector<vector<int> > *slvs,int f) {
          ^
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/lib64/qt4/mkspecs/linux-g++ -I. -I/usr/include/QtCore -I/usr/include/QtGui -I/usr/include -Ibuild -o build/consensus.o src/consensus.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/lib64/qt4/mkspecs/linux-g++ -I. -I/usr/include/QtCore -I/usr/include/QtGui -I/usr/include -Ibuild -o build/genes.o src/genes.cpp
src/genes.cpp: In constructor ‘wb::Genes::Genes(wb::Alignment*, char*, char*)’:
src/genes.cpp:34:35: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
             fscanf(mapf,"%d",&buf);
                                   ^
src/genes.cpp:53:42: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
             fscanf(genes,"%d %d",&f1,&f2);
                                          ^
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/lib64/qt4/mkspecs/linux-g++ -I. -I/usr/include/QtCore -I/usr/include/QtGui -I/usr/include -Ibuild -o build/hashcell.o src/hashcell.cpp
src/hashcell.cpp: In member function ‘void wb::HashCell::addNode(wb::Tree*)’:
src/hashcell.cpp:51:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (l>=t->recMap->size) break;
                               ^
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/lib64/qt4/mkspecs/linux-g++ -I. -I/usr/include/QtCore -I/usr/include/QtGui -I/usr/include -Ibuild -o build/move_ages.o src/move_ages.cpp
src/move_ages.cpp: In member function ‘virtual void wb::Move_ages::move(wb::Param*)’:
src/move_ages.cpp:60:21: warning: suggest braces around empty body in an ‘else’ statement [-Wempty-body]
             } else  ;//printf("Age change rejected because out of range\n");
                     ^
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/lib64/qt4/mkspecs/linux-g++ -I. -I/usr/include/QtCore -I/usr/include/QtGui -I/usr/include -Ibuild -o build/move_delta.o src/move_delta.cpp
src/move_delta.cpp:24:5: warning: unused parameter ‘p’ [-Wunused-parameter]
     Move_delta::Move_delta(gsl_rng * rng,Param * p):Move(rng) {
     ^
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/lib64/qt4/mkspecs/linux-g++ -I. -I/usr/include/QtCore -I/usr/include/QtGui -I/usr/include -Ibuild -o build/move_gap.o src/move_gap.cpp
src/move_gap.cpp:24:5: warning: unused parameter ‘p’ [-Wunused-parameter]
     Move_gap::Move_gap(gsl_rng * rng,Param * p) : Move(rng) {}
     ^
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/lib64/qt4/mkspecs/linux-g++ -I. -I/usr/include/QtCore -I/usr/include/QtGui -I/usr/include -Ibuild -o build/move_hidden.o src/move_hidden.cpp
src/move_hidden.cpp:25:5: warning: unused parameter ‘p’ [-Wunused-parameter]
     Move_hidden::Move_hidden(gsl_rng * rng,Param * p) : Move(rng)
     ^
src/move_hidden.cpp: In member function ‘void wb::Move_hidden::forwardfast(wb::Param*, wb::Tree*)’:
src/move_hidden.cpp:127:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (unsigned int i=0;i<L;i++)
                                 ^
src/move_hidden.cpp:133:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (unsigned int j=0;j<nbstates;j++) gsl_vector_set(probas,j,gsl_vector_get(pbeg,j));
                                         ^
src/move_hidden.cpp:137:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     for (unsigned int j=0;j<nbstates;j++) gsl_vector_set(probas,j,gsl_vector_get(probas,j)*gsl_matrix_get(a,j,j)*gsl_matrix_get(e,j,msgs[k]));
                                             ^
src/move_hidden.cpp:132:21: warning: unused variable ‘top’ [-Wunused-variable]
                 int top=0,left=0,right=0;
                     ^
src/move_hidden.cpp:132:27: warning: unused variable ‘left’ [-Wunused-variable]
                 int top=0,left=0,right=0;
                           ^
src/move_hidden.cpp:132:34: warning: unused variable ‘right’ [-Wunused-variable]
                 int top=0,left=0,right=0;
                                  ^
src/move_hidden.cpp: In member function ‘gsl_matrix* wb::Move_hidden::forward(wb::Param*)’:
src/move_hidden.cpp:169:62: error: taking address of temporary [-fpermissive]
             Util::normalize(&(gsl_matrix_column(f,i+1).vector));
                                                              ^
src/move_hidden.cpp: In member function ‘void wb::Move_hidden::backward(wb::Param*, gsl_matrix*, wb::Tree*)’:
src/move_hidden.cpp:202:17: warning: unused variable ‘d’ [-Wunused-variable]
             int d=gsl_vector_int_get(p->a->polySites,old)- gsl_vector_int_get(p->a->polySites,old-1);
                 ^
src/move_hidden.cpp: In member function ‘void wb::Move_hidden::makee(wb::Param*, wb::Tree*)’:
src/move_hidden.cpp:423:59: error: taking address of temporary [-fpermissive]
             Util::normalize(&(gsl_matrix_row(e,i+1).vector));
                                                           ^
make: *** [build/move_hidden.o] Error 1

From this there are two errors, and the rest are warnings.
The errors are:
src/move_hidden.cpp: In member function ‘gsl_matrix* wb::Move_hidden::forward(wb::Param*)’:
src/move_hidden.cpp:169:62: error: taking address of temporary [-fpermissive]
Util::normalize(&(gsl_matrix_column(f,i+1).vector));

src/move_hidden.cpp: In member function ‘void wb::Move_hidden::makee(wb::Param_, wb::Tree_)’:
src/move_hidden.cpp:423:59: error: taking address of temporary [-fpermissive]
Util::normalize(&(gsl_matrix_row(e,i+1).vector));

Do you know if adding or removing a flag from the MakeFile could solve this issue?
Thank you

Edit:
I added the flag -fpermissive to the CXXFLAGS and it compiled, but quoting the standard:

§5.3.1 Unary operators, Section 3

The result of the unary & operator is a pointer to its operand. The operand shall be an lvalue or a qualified-id.

I'm not very familiar with C++, so I don't really know if this is a problem or not. I am just leaving it there in case it helps you.

When I read the guide of ClonalFrameML I could not figure out which file I have 
to use as input to generate start newick tree: xmfa file from mauve?

Thanks
Joaquim

Original issue reported on code.google.com by [email protected] on 16 Apr 2015 at 9:21

I notice the example Saureus.fasta whole genome alignment has no Ns or gaps in 
it, which suggests every column is "core". 

However there is a core.txt and noncore.txt sites file.

Did you patch the N/- chars with bases from the reference?

Is that necessary, or can cfML handle them itself?

Torsten

Original issue reported on code.google.com by [email protected] on 17 Feb 2015 at 3:38

Hi Xavier,

I'm trying to use ClonalFrameML, but I keep getting errors.

First, I performed the multiple alignment using parsnp.

Then I tried to use my parsnp files to run ClonalFrameML. Here is my code:
./ClonalFrameML /home/nick/Desktop/server/parsnp.tree /home/nick/Desktop/server/parsnp.xmfa output -xmfa_file true

And this was my output:
ClonalFrameML v1.0-19-g9488a80
xmfa_file = true
Finished reading in control file.

Read 17 sequences of length 1460560 sites from /home/nick/Desktop/server/parsnp.xmfa
ERROR: convert_NewickTree_to_marginal_tree(): Newick tree tip label 'GCF_000270445.1_ASM27044v1_genomic.fna' was not expected

Since parsnp didn't seem to work with ClonalFrameML, I tried using mauve instead.
When trying to use the mauve files as input, I entered this code:
./ClonalFrameML /home/nick/Desktop/server/"mauve output"/ml.guide_tree /home/nick/Desktop/server/"mauve output"/ml.alignment output -xmfa_file true

And this was my output:
ClonalFrameML v1.0-19-g9488a80
xmfa_file = true
Finished reading in control file.

Read 19 sequences of length 1721579 sites from /home/nick/Desktop/server/mauve output/ml.alignment
ERROR: Token: (
Found left bracket but no right bracket

Please let me know if you think you know what the problem might be.

Thanks,
Nick

To update the conda/brew packages we need a new release.

Also needed as version on code.google seemed to be "1.7" but here it is "1.0" ?

Could it be 1.8 ?

Hi,

the cfml_results.R script is throwing an error, and I'm having a difficult time figuring out how to resolve it. I've attached the CFML output files that I'm feeding into the script. I'm using R v3.3.0, ape v3.5, and phangorn v2.0.4. Thanks in advance for your help and the useful software!

best,
shane

Warning message:
NAs introduced by coercion
Warning message:
In ifelse(is.na(as.numeric(rownames(wh.mut))), rownames(wh.mut), :
NAs introduced by coercion
Warning message:
In ifelse(is.na(as.numeric(rownames(wh.mut))), rownames(wh.mut), :
NAs introduced by coercion
null device
1
[[1]]
NULL
[[2]]
NULL
[[3]]
NULL
[[4]]
NULL
[[5]]
NULL
[[6]]
NULL
[[7]]
NULL
[[8]]
NULL
[[9]]
NULL
[[10]]
NULL
[[11]]
NULL
[[12]]
NULL
[[13]]
NULL
[[14]]
NULL
[[15]]
NULL
[[16]]
NULL
[[17]]
NULL
[[18]]
NULL
[[19]]
NULL
[[20]]
NULL
[[21]]
NULL
[[22]]
NULL
null device
1
CFML_phyml_output.em.txt
CFML_phyml_output.emsim.txt
CFML_phyml_output.importation_status.txt
CFML_phyml_output.position_cross_reference.txt
core_sites.txt
CFML_phyml_output.labelled_tree.newick.txt
CFML_phyml_output.ML_sequence.fasta.txt

It appears that CFML does not accept XMFA as formatted by Mauve. It is unclear 
how this file should be formatted.

What steps will reproduce the problem?
1. Using standard Mauve-formatted XMFA, I get the error message:
ERROR: readXMFA(): File ../CC11_SGW_Complete.xmfa did not begin with '>'

2. I can strip out the comment lines (#), but that removes the sample naming 
key (i.e. samples are named 1,2,3 ... which is not what I used in my guide tree)

How are XMFA files supposed to be formatted? Will it work if we use the 
"seqnum" identifiers for the guide tree? Or conversely, could we replace the 
"seqnum" identifiers in the XMFA with the sample names?

Thanks.



Please provide any additional information below.

Original issue reported on code.google.com by [email protected] on 29 May 2015 at 4:12

Dear Dr. Didelot,
When running the version 1.2 compiled from the source, with the flag -fpermissive on my Linux Redhat 7.1 server with GCC version 4.8.3

I obtained the following error:

/source_installers/ClonalFrameML/ClonalFrame_precompiled/ClonalFrame -w RAxML_bestTree.guide_tree MWGSA.fasta clonal_frame_results
This is ClonalFrame version 1.2
Got seed 2847455674 from /dev/urandom
N=122, b=0, L=0
gsl: init_source.c:46: ERROR: failed to allocate space for block data
Default GSL error handler invoked.
Aborted

My data has 122 sequences and the alignment has a length of 3008183 positions, including gaps.
The server has 64GB in RAM and the file with the alignment has an approximate size of 500MB

Thank you

Hello,
Just trying to compile this on a fedora 19 desktop and running into this error after I run 'make':

/bin/echo "#define ClonalFrameML_GITRevision "git describe --tags"" > version.h
g++ -O3 -I./ -I./myutils -I./coalesce -c -o main.o main.cpp
In file included from coalesce/coalesce.h:22:0,
from main.h:25,
from main.cpp:20:
./coalesce/coalescent_control.h: In member function ‘Control& Control::read_input(char_)’:
./coalesce/coalescent_control.h:121:87: warning: deprecated conversion from string constant to ‘char_’ [-Wwrite-strings]
if(!control_file.got_required)error("Not all necessary items found in control file");
^
./coalesce/coalescent_control.h:124:85: warning: deprecated conversion from string constant to ‘char_’ [-Wwrite-strings]
if(!control_file.got_required)error("read_input(): necessary parameters not found");
^
./coalesce/coalescent_control.h:128:69: warning: deprecated conversion from string constant to ‘char_’ [-Wwrite-strings]
if(ntimes.size()!=nsamp)error("ntimes inconsistent in size with n");
^
./coalesce/coalescent_control.h:135:65: warning: deprecated conversion from string constant to ‘char_’ [-Wwrite-strings]
if(len.size()!=loci)error("len inconsistent in size with loci");
^
./coalesce/coalescent_control.h:136:87: warning: deprecated conversion from string constant to ‘char_’ [-Wwrite-strings]
if(state_freq.size()!=n_states)error("state_freq inconsistent in size with n_states");
^
./coalesce/coalescent_control.h:144:81: warning: deprecated conversion from string constant to ‘char_’ [-Wwrite-strings]
else if(seq_len!=ind_seq_len) error("seq_len and the sum of len do not equate");
^
./coalesce/coalescent_control.h:159:92: warning: deprecated conversion from string constant to ‘char_’ [-Wwrite-strings]
if(!one_or_the_other)error("read_input(): neither state_M or state_rel_mut_rate received");
^
./coalesce/coalescent_control.h:162:82: warning: deprecated conversion from string constant to ‘char_’ [-Wwrite-strings]
if(state_M.size()!=n_states)error("state_M inconsistent in size with n_states");
^
./coalesce/coalescent_control.h:170:104: warning: deprecated conversion from string constant to ‘char_’ [-Wwrite-strings]
if(state_rel_mut_rate.size()!=n_states)error("state_rel_mut_rate inconsistent in size with n_states");
^
./coalesce/coalescent_control.h: In member function ‘Control& Control::vector_to_Matrix(std::vector, myutils::Matrix, int, int)’:
./coalesce/coalescent_control.h:202:94: warning: deprecated conversion from string constant to ‘char_’ [-Wwrite-strings]
if((int)vec->size()<(rows_cols))error("vector_to_Matrix(): vector too small to fill matrix");
^
./coalesce/coalescent_control.h:203:93: warning: deprecated conversion from string constant to ‘char_’ [-Wwrite-strings]
if((int)vec->size()>(rows_cols))error("vector_to_Matrix(): vector too large to fit matrix");
^
./coalesce/coalescent_control.h: In member function ‘Control& Control::read_mut_matrix(myutils::Matrix&, std::vector&)’:
./coalesce/coalescent_control.h:224:73: warning: deprecated conversion from string constant to ‘char_’ [-Wwrite-strings]
if(G.nrows()!=G.ncols())error("read_mut_matrix(): not a square matrix");
^
./coalesce/coalescent_control.h:231:72: warning: deprecated conversion from string constant to ‘char_’ [-Wwrite-strings]
if(G[i][j]<0.0)error("read_mut_matrix(): negative rates in matrix");
^
./coalesce/coalescent_control.h:234:69: warning: deprecated conversion from string constant to ‘char_’ [-Wwrite-strings]
if(rowsum!=-G[i][i]) error("read_mut_matrix(): not a rate matrix");
^
./coalesce/coalescent_control.h:239:83: warning: deprecated conversion from string constant to ‘char_’ [-Wwrite-strings]
if(pi.size()!=n_states)error("read_mut_matrix(): pi inconsistent in size with G");
^
./coalesce/coalescent_control.h:243:76: warning: deprecated conversion from string constant to ‘char_’ [-Wwrite-strings]
if(pi[i]<0.0)error("read_mut_matrix(): negative equilibrium frequencies");
^
./coalesce/coalescent_control.h:246:66: warning: deprecated conversion from string constant to ‘char_’ [-Wwrite-strings]
if(pisum!=1.0)error("read_mut_matrix(): pi does not sum to one");
^
In file included from ./coalesce/coalescent_process.h:35:0,
from coalesce/coalesce.h:23,
from main.h:25,
from main.cpp:20:
./coalesce/coalescent_record.h: In member function ‘mt_node* marginal_tree::coalesce(double&, int&, int&)’:
./coalesce/coalescent_record.h:119:58: warning: deprecated conversion from string constant to ‘char_’ [-Wwrite-strings]
error("coalesce(): cannot coalesce a node with itself");
^
./coalesce/coalescent_record.h:126:57: warning: deprecated conversion from string constant to ‘char_’ [-Wwrite-strings]
error("coalesce(): called when no longer segregating");
^
./coalesce/coalescent_record.h: In member function ‘mt_node* marginal_tree::migrate_coalesce(double&, int&, int&)’:
./coalesce/coalescent_record.h:148:58: warning: deprecated conversion from string constant to ‘char_’ [-Wwrite-strings]
error("coalesce(): cannot coalesce a node with itself");
^
./coalesce/coalescent_record.h:155:57: warning: deprecated conversion from string constant to ‘char_’ [-Wwrite-strings]
error("coalesce(): called when no longer segregating");
^
g++ -o ClonalFrameML main.o

Any ideas what is going on?
Thanks!
~josh

Hi

I have used CFML previously to detect recombination from a core genome alignment. However, I am now wondering whether it is possible to use it for a core gene alignment? (I have used Roary to determine the core genes).

Thanks

Dear Dr. Didelot and Colleagues,

I got the following error when I tried to ru CLFML with per-branch model and 
custom initial_values for for R/theta, 1/delta and nu

ClonalFrameML version 1.25
kappa = 2.36
embranch = true
embranch_dispersion = 0.1
xmfa_file = true
initial_values = 0.101946
ERROR: Syntax error in ArgumentWizard::read_label: option must be prefixed with 
a '-'

Command line:

ClonalFrameML FcC_smatrix_fixed.phy_phyml_tree_rooted.txt 
mbovis_core_aln_header_fixed2.xmfa mbovisRefinedRun_step2 -kappa 2.360 
-embranch true -embranch_dispersion 0.1 -xmfa_file true -initial_values 
"0.101946 0.0465039 0.105836" > mbovisRefinedRun_step2.log.txt

I could be able to figure out where is the command error. 

Best regards
Joaquim

Original issue reported on code.google.com by [email protected] on 19 Apr 2015 at 6:29

We've run ClonalFrameML through the
ClonalFrameML newick_file seq_file output_prefix [OPTIONS]
step, getting the appropriate output files. However running

Rscript.exe cfml_results.R anophelisoutbreakclone2.output

gives the following errors:

Read 3918024 items
Read 30 items
Warning message:
NAs introduced by coercion
Warning message:
In ifelse(is.na(as.numeric(tree$tip.label)), tree$tip.label, paste("C0000", :
NAs introduced by coercion
Warning message:
In ifelse(is.na(as.numeric(rownames(wh.mut))), rownames(wh.mut), :
NAs introduced by coercion
Error in pdf(file = "/dev/null", width = 14, height = 7) :
cannot open file '/dev/null'
Execution halted

We are running R-3.2.5 64-bit on a 64-bit Windows 10 machine with the latest ape and phangorn loaded. Searching turned up nothing except it involves the as.numeric function.

Also, if problem is with running a Windows machine, let me know. Thanks.
Peter

@xavierdidelot I am still confused by your answer in #45

The latest binary you or Daniel provide for Linux here
https://github.com/xavierdidelot/ClonalFrameML#download
is 1.25

./ClonalFrameML.Ubuntu.12.04.2.LTS  | head -n 1
ClonalFrameML version 1.25

Does this mean we are using an OLD version?

Hi,

We are trying to test if our pipeline is correct so we apply the 
tutorial-provided command to the example data set 
http://www.danielwilson.me.uk/files/cfml.tgz

We run the following command
./ClonalFrameML Saureus.phyML.newick Saureus.fasta example.output -kappa 
4.967695 -emsim 100 -ignore_user_sites Saureus.non-core-sites.txt > 
example.log.txt

The numbers we get are 
Parameter   Posterior Mean  Posterior Variance  a_post  b_post
R/theta 0.143922    1.24819e-06 16594.7 115304
1/delta 0.00284445  4.87804e-10 16586.3 5.83112e+06
nu  0.0146705   2.92734e-09 73522.2 5.01155e+06

It seems the one we got (R/theta=0.14, delta=1/0.0028 =315bp and nu=0.015) is 
different from what the paper shows (R/θ = 0.215, δ = 183bp and ν = 
7.20×10−3) @ (Page 12 of "ClonalFrameML: Efficient Inference of 
Recombination in Whole Bacterial Genomes") 

Could you please provide the expected results of the sample data? If what we 
got is not the right ones, can you please tell us what is the error?

Thanks and best regards,
Jessie

Original issue reported on code.google.com by [email protected] on 3 Jun 2015 at 6:01

Dear Dr. Didelot,

I have encountered this error after the execution of ClonalFrame version 1.-178:
ClonalFrameML RAxML_bestTree.guide_tree MWGSA.fasta clonalframe_MWGSA
ClonalFrameML version 1.-178
Finished reading in control file.

Read 122 sequences of length 3008183 sites from MWGSA.fasta
ERROR: convert_NewickTree_to_marginal_tree(): Newick tree tip label AMAH01_1 was not expected

I am sure my tree does not have any bootstrap values in it.
The fasta file with alignment is just a regular fasta file, not an extended one, I did not obtain the alignment with mauve as you suggest in the ClonalFrame Manual, and I'm sure that in the fasta file in the headers lines for each sequence, there is only the id of each sequence.

Could you please give me some idea on what might be happening with my data?

Thank you

Hi Xavier,

I'm having some trouble running ClonalFrameML on my data. My newik tree and xmfa file have been obtained by Mauve and I'm having the same error as others :

Read 21 sequences of length 1063625 sites from ClonalFrame_Lp_genomes/GWAS_alignment.xmfa
ERROR: convert_NewickTree_to_marginal_tree(): Newick tree tip label seq5 was not expected

So I followed your advice on topic #18
and simplifyed my headers (ex : >seq5).

But it was not enough to solve the error.

Then I noticed the solution of topic #17, but my tree doesn't seem to have bootstrap values.

Then going back to the end of topic #18, I noticed than in my xmfa file, as simianraticus, most of blocks doesn't have the sequence of all genomes. =/.

Did you find out a solution for that ? Would you recommand to use an other software than Mauve to produce the xmfa file and the newick tree ?

Thank you very much for your help :)

Hi,
Following on one from one of the earlier issues, regarding the use of XMFA 
files.  For some reason, when I follow the below usage, it doesn't like the 
XMFA file i supply?!?

Usage:
progressiveMauve --output=full_alignment.xmfa merged.fa

stripSubsetLCBs full_alignment.xmfa full_alignment.xmfa.bbcols 
core_alignment.xmfa 500

ClonalFrameML merged.aligned.guide_tree  core_alignment.xmfa  example.out 
-xmfa_file true

Error:
ClonalFrameML version 1.25
xmfa_file = true
Finished reading in control file.

ERROR: readXMFA(): File 
/mnt/data123/data1/raju/raju/Cdiff_strains/A027/A027s_test_170415_STRIPPED_CORE.
xmfa did not begin with '>'

Any help to get this working would be very much appreciated.
Thanks,
Raj

Original issue reported on code.google.com by [email protected] on 20 Apr 2015 at 10:59

Dear colleagues,

I got the following error when I ran ClonalFrameML

ClonalFrameML version 1.25
embranch = true
embranch_dispersion = 0.1
show_progress = true
xmfa_file = true
Finished reading in control file.

Read 30 sequences of length 4323381 sites from mbovis_core_aln_header_fixed.xmfa
ERROR: convert_NewickTree_to_marginal_tree(): Newick tree tip label 
Mbovis_95_01315_S6_USA was not expected

Could you help me to fix this error?

Best wishes,
Joaquim

Original issue reported on code.google.com by [email protected] on 17 Apr 2015 at 6:04

Dear Dr Didelot

From reading issue #35, I understand that the labelled_tree.nwk is not created from simply removing all recombination, but rather takes into account both mutation and recombination. Can I obtain the sequence fasta that CFML has used to create this phylogeny?
I would like to use BEAST, and therefore adjust my MSA to account for recombination.

Kind regards

Stan

Could you please help us resolve this problem? We run the following command in 
the linux system, but the software can't load the newick file successfully.

$ ClonalFrameML test2.nwk Ruegeria.mauve.xmfa example.out -xmfa_file true

ClonalFrameML version 1.-178
xmfa_file = true
Finished reading in control file.

Read 3 sequences of length 6166140 sites from Ruegeria.mauve.xmfa
ERROR: convert_NewickTree_to_marginal_tree(): Newick tree tip label 1A00367 was 
not expected

--------------------------------------------
The headers of the xmfa file are

> 1:328529-587434 + 1A00326.fasta
......
> 2:480132-758035 + 1A00367.fasta
.......
> 3:383272-630755 + 1A00371.fasta
.......
=
> 1:587435-722709 - 1A00326.fasta
......
> 2:3437039-3569932 + 1A00367.fasta
.......
> 3:630756-751222 - 1A00371.fasta
.......
=
..........

-----------------------------------
we have tried the following newick files but still got the same type of error

test1.nwk
(1A00367:0.5,(1A00371:0.0462279,1A00326:0.0223751):0.0223751);

test2.nwk
(2:0.5,(3:0.0462279,1:0.0223751):0.0223751);



Thanks so much!

Original issue reported on code.google.com by [email protected] on 25 May 2015 at 10:45

Dear Xavier/Daniel,

After testing the sample data, I got the same result as GoogleCodeExporter did.
#16
Could you please also tell me the reason?

In addition to this, I run the following command with cfml_results_2.R in cfml.tgz.
Rscript cfml_results_2.R Exam core-sites.txt
I got the pdf Exam.cfml.pdf, but the Grey areas do not exist, is the grey areas was added later by other tool?
Exam.cfml.pdf

Best wishes,
YangChao

Dear Xavier,

I want to know how the labelled_tree.newick is constructed, is the recombination region in importation_status.txt removed and then the rest region was used to reconstruct the tree?

If I want to use SNPs in non-recombinant regions to reconstruct tree, what should I do?
Is it right? 1.remove the recombination region in importation_status.txt. 2.call SNPs in the rest region. 3. reconstruct phylogenetic tree

Best regards,
Yangchao

• I currently have a binary which says 1.7
• I downloaded binary today and it says 1.25
• The latest github code release says 1.0

Is 1.25 newer than 1.7 ?

What version of binary does the 1.0 github release source code correspond to?

Dear Xavier/Daniel,

I am having difficulty with running ClonalframeML. I have the appropriate input files e.g. a starting tree (.txt) in Newick format generated by phyml and an alignment of the sequences in fasta format.

When i run the command
./ClonalframeML /home/SNV1.txt /home/SNV1.fa SNV1_out

I get the following error

ClonalFrameML version 1.25
Finished reading in control file.

Read 20 sequences of length 4290252 sites from /home/SNV1.fa
ERROR: convert_NewickTree_to_marginal_tree(): Newick tree tip label 1.000000 was not expected

I did see that someone else had this error (#7) and that is was resolved offline.
Please can you advise.

Best wishes
Daniel

Hi：
   Thanks for your tools help me to sovle my research project. I used your software and  got the results,but I am amazing about your result file of importation_status.txt.I have ten samples, i got the begining and end of genome ocation about recombinantion for my samples,but also got other Node in the importation_status.txt file,the Node column name is consisted of  "Node_" and number.What are thses Nodes ?I have nothing with them.
Thanks

Original issue reported on code.google.com by [email protected] on 22 Apr 2015 at 1:19

using Clonal Frame 1.7 and trying to run directly from the output of parsnp, which produces a tree and multifasta file of the aligned genomes. I get an error, which looks like the program is having trouble reading the tree:

`$ ClonalFrameML parsnp.tree parsnp.fasta output -kappa 2
ClonalFrameML version 1.7
kappa = 2
Finished reading in control file.

Read 526 sequences of length 2233330 sites from parsnp.fasta
ERROR: convert_NewickTree_to_marginal_tree(): Newick tree tip label 0.920 was not expected`

There are no tip labels with this name but there are internal branch lengths. Interested to know if anyone else has seen this?

What steps will reproduce the problem?
1. I downloaded the mac executable
2. I ran the command ./ClonalFrame.Mac.10.7.5 
Mels_MLSA7_genomes_noST10_ML.newick Mels_MLSA7_genomes_noST10_aln.fas outCFML
3. I got an error reading the newick "Expected trailing semi-colon but none 
found"
4. I thought perhaps because PhyML put spaces in my nwk it messed the reading 
up. Removed spaces - same error
5. I removed dashes because some programs have issues with dashes in names and 
retried - same error.
6. It just is not recognizing the ending semi-colon to my file.

What is the expected output? What do you see instead?

I am trying to get the program working, yet it will not recognize the semi 
colon at the end of the nwk file.

What version of the product are you using? On what operating system?

10.7.5

MacOSX version 10.7.5, 2.4 GHz Intel Core 2 Duo, Memory 4GB 1067 MHz DDR3


Please provide any additional information below.

Original issue reported on code.google.com by [email protected] on 3 Apr 2015 at 7:35

Attachments:

• Mels_MLSA7_genomes_noST10_aln.fas
• Mels_MLSA7_genomes_noST10_ML.nwk

Hi,
Following on one from one of the earlier issues, regarding the use of XMFA 
files.  For some reason, when I follow the below usage, it doesn't like the 
XMFA file i supply?!?

Usage:
progressiveMauve --output=full_alignment.xmfa merged.fa

stripSubsetLCBs full_alignment.xmfa full_alignment.xmfa.bbcols 
core_alignment.xmfa 500

ClonalFrameML merged.aligned.guide_tree  core_alignment.xmfa  example.out 
-xmfa_file true

Error:
ClonalFrameML version 1.25
xmfa_file = true
Finished reading in control file.

ERROR: readXMFA(): File 
/mnt/data123/data1/raju/raju/Cdiff_strains/A027/A027s_test_170415_STRIPPED_CORE.
xmfa did not begin with '>'

Any help to get this working would be very much appreciated.
Thanks,
Raj

Original issue reported on code.google.com by [email protected] on 20 Apr 2015 at 10:58

Dear Xavier/Daniel,

I want to know the exact meaning of -ignore_user_sites, is the region ignored involved in subsequent analysis or not ?

If the region is discarded, is there any difference between an alignment which the region is striped and an alignment with the -ignore_user_sites option?

You recommend that we should extract the core from the file generated with mauve, is this means that I had better use core genome sequence alignment, not the complete genome sequence alignment with -ignore_user_sites option to ignore non-core sites ?

Best wishes,
YangChao

Xavier,

Will CFML ever support non strictly bifurcating trees?

If not, do you have a simple/neat way to convert an N-ary tree into a 2-ary 
tree?

I've found the ETE2 library can do it but that is a heavyweight Python library 
to expect people to install.

Torsten

Original issue reported on code.google.com by [email protected] on 28 May 2015 at 8:09

As a test case I have 10 genomes, aligned with progressiveMauve, core genome 
extracted with stripsubsetLCBs. According to the manual ClonalFrameML should 
accept XMFA, but it doesn't.

progressiveMauve --output=full_alignment.xmfa merged.fa

stripSubsetLCBs full_alignment.xmfa full_alignment.xmfa.bbcols 
core_alignment.xmfa 500


ClonalFrameML merged.aligned.guide_tree  core_alignment.xmfa  example.out 
-kappa 4.967695 -emsim 100
ClonalFrameML version 1.11
kappa = 4.96769
emsim = 100
Finished reading in control file.

ERROR: DNA::readFASTA_1pass(): File core_alignment.xmfa did not begin with '>'

Should I convert the xmfa file to fasta and use that as input?

Original issue reported on code.google.com by [email protected] on 16 Dec 2014 at 7:53

Hi,

I'm trying to run clonalframeML on a core gene alignment consisting of 902 individual core genes from 102 bacterial strains. I have generated an xmfa file with each alignment separated with a "=" . I am getting this error output:

ClonalFrameML v1.0-19-g9488a80
xmfa_file = true
ignore_incomplete_sites = true
emsim = 100
Finished reading in control file.

Read 102 sequences of length 1589752 sites from xmfa3
ERROR: FASTA_to_nucleotide(): unsupported base

I have checked and every genome is included in the 902 alignments. I think the error has something to do with the format of my xmfa file as when I import it into the program geneious it says there is an ambiguous base at the end of the last sequence of each alignment (so next to the "="). I have tried with the sequences wrapped/unwrapped and with/without empty lines between each sequence.

Many thanks,
Michelle

Hi Xavier,

In some recombination detection softwares such as Gubbin which identifies loci containing elevated densities of base substitutions, they can't distinguish elevated densities of polymorphisms arising through
recombination from other potential causes such as mutational ‘hotspots’, or regions under relaxed or positive selection, on branches representing long periods of divergence.

In my opinion, there is no such biases in ClonalFrameML, am I right?

Best wishes,
Yangchao

To get an XMFA file that works in ClonalFrame, the original XMFA output from MAUVE will not work. After running StripsubsetsLCB as described here the StripsubsetsLCB output XMFA file (originally from MAUVE) has the correct lengths format, but the header lines often have additional information such as genome position numbers that must be removed, leaving only the organism name (e.g. >S. aureus).
Below is a short script to remove the genome position numbers up to the organism name, if and ONLY if, your headers look like mine (for example):

2:3289121-3291310 + e.anophelisNUHP1.fas

sed can be used on the StripsubsetsLCB output XMFA file:
sed -r 's/^>..* -*/>/' your_xmfa_file.xmfa
I'm not a great coder so please improve on this one-liner. It seems to work for me but doesn't have any fail safes and I'm running Python in a bash console on Windows 10 (not the built-in Ubuntu yet).

pete

Hi,

After running clonalframeML with default options I would like to compare the output tree (labelled_tree.newick) with the input tree (RAxML.newick) to see how the program has altered the topology and branch lengths (if at all).

Only when I open in a tree viewer like MEGA I see that the clonalframeML tree is rooted and the layout is quite different from the input tree and a little confusing to read. I ideally need mid-point roots (or at least the option to add and remove myself). My question is how can I unroot the output tree to allow for a sensible comparison? Was there a flag to pass during invoking clonalframeML?

I hope this makes sense. I have attached the input and output trees (appended with .txt to allow attaching to this message)

Input tree (RAxML)
RAxML_bestTree.cd-raxml-8.nwk.txt
.
Output tree (ClonalframeML)
gethoms4_cd-raxml-8_cfml.labelled_tree.newick.txt

Any help you can provide would be much appreciated.
Kind regards
Dan

Dear Xavier,

when using CFML with my subject, I got the Parameter like that: R/theta 0.0925738, 1/delta 0.000199615 , nu 0.0143449, it seems that 1/delta was too small, this is abnormal. Could you tell me what factors may lead to a very small 1/delta?

-kappa 3.62 -emsim 100 -ignore_user_sites xxx was used for the analysis.

Best regards,
Yangchao

Hi Xavier,

I'm having problems to run ClonalFrameML ( v1.0-19-g9488a80) on my data...

I generated the alignment file with mauve, so I'm using the .xmfa file as an input by adding the option "-xmfa_file true". The tree file looks like this: (sample1,((sample2,sample3),sample4));. The names in the headers of the alignment file match the ones in the tree. After executing the command, I get the following error message:

ERROR: Token: sample1,((sample2,sample3
Too few right brackets

I've followed different advises found along the comments here but nothing seems to work: I'm using the core alignment, there are no white spaces after the ">", I converted the end lines, I also tried to work with a concat fasta file... What else can I do? I'm running out of ideas...

Thanks for you help!

/Andrea

Dear Xavier/Daniel,

I have got results like these:
Parameter Posterior Mean Posterior Variance a_post b_post
R/theta 0.957746 0.0558031 16.4378 17.163
1/delta 0.00720444 3.23E-06 16.085 2232.65
nu 0.737493 0.000592833 917.452 1244.02
s204 0.000181416 1.66E-08 1.9874 10955
s210 0.000270652 2.47E-08 2.96495 10954.8

what's the meaning of a_post and b_post