computations / root_digger Goto Github PK

I would like to be able to export a file which only contains the output tree so I can easily pipe it into other tools in my workflow.

When I run root digger it prints a log and the output tree to the console. I can direct stdout to a file but then the file will contain both the log and the tree. I tried --silent which moved things in the right direction but the tool still returned [0.02] INFO: Early stop is enabled as well. Ideally I wouldn't want to use --silent because I would like to see the log. I also looked for something like --outfile in the options but couldn't find anything. Any ideas how I could export the tree? Many thanks.

Hi,

I'm trying to install Root Digger on my mac and have run into some errors. At first my problem was not having installed googletest, but I think I have that sorted now. I'm not experienced with cmake etc. Can you see what I'm doing wrong?

Many thanks,
Bryony

bbraschi@bbraschi-ml root_digger % make
-- The C compiler identification is AppleClang 13.0.0.13000029
-- The CXX compiler identification is AppleClang 13.0.0.13000029
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found Git: /usr/bin/git (found version "2.30.1 (Apple Git-130)")
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Found OpenMP_C: -Xclang -fopenmp (found version "5.0")
-- Found OpenMP_CXX: -Xclang -fopenmp (found version "5.0")
-- Found OpenMP: TRUE (found version "5.0")
-- SSE enabled. To disable it, run cmake with -DENABLE_SSE=false
-- AVX enabled. To disable it, run cmake with -DENABLE_AVX=false
-- AVX2 enabled. To disable it, run cmake with -DENABLE_AVX2=false
Non-rev enabled
-- coraxlib libraries: corax_static
-- Found GTest: /usr/local/lib/cmake/GTest/GTestConfig.cmake (found version "1.11.0")
-- Configuring done
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:

BENCHMARK_ENABLE_LTO

-- Build files have been written to: /Users/bbraschi/Scratch/root_digger/build
[ 1%] Building C object lib/lbfgsb/CMakeFiles/lbfgs_lib.dir/lbfgsb.c.o
[ 2%] Building C object lib/lbfgsb/CMakeFiles/lbfgs_lib.dir/linesearch.c.o
[ 3%] Building C object lib/lbfgsb/CMakeFiles/lbfgs_lib.dir/linpack.c.o
[ 4%] Building C object lib/lbfgsb/CMakeFiles/lbfgs_lib.dir/miniCBLAS.c.o
[ 5%] Building C object lib/lbfgsb/CMakeFiles/lbfgs_lib.dir/subalgorithms.c.o
[ 6%] Linking C static library liblbfgs_lib.a
[ 6%] Built target lbfgs_lib
[ 7%] Building C object lib/coraxlib/src/corax/CMakeFiles/corax_obj.dir/core/common.c.o
[ 8%] Building C object lib/coraxlib/src/corax/CMakeFiles/corax_obj.dir/core/parsimony.c.o
[ 9%] Building C object lib/coraxlib/src/corax/CMakeFiles/corax_obj.dir/core/partition.c.o
[ 10%] Building C object lib/coraxlib/src/corax/CMakeFiles/corax_obj.dir/core/repeats.c.o
[ 11%] Building C object lib/coraxlib/src/corax/CMakeFiles/corax_obj.dir/io/binary.c.o
[ 12%] Building C object lib/coraxlib/src/corax/CMakeFiles/corax_obj.dir/io/binary_io_operations.c.o
[ 13%] Building C object lib/coraxlib/src/corax/CMakeFiles/corax_obj.dir/io/fasta.c.o
[ 15%] Building C object lib/coraxlib/src/corax/CMakeFiles/corax_obj.dir/io/maps.c.o
[ 16%] Building C object lib/coraxlib/src/corax/CMakeFiles/corax_obj.dir/io/output.c.o
[ 17%] Building C object lib/coraxlib/src/corax/CMakeFiles/corax_obj.dir/io/phylip.c.o
[ 18%] Building C object lib/coraxlib/src/corax/CMakeFiles/corax_obj.dir/io/utree_ascii.c.o
[ 19%] Building C object lib/coraxlib/src/corax/CMakeFiles/corax_obj.dir/io/utree_newick.c.o
[ 20%] Building C object lib/coraxlib/src/corax/CMakeFiles/corax_obj.dir/io/utree_svg.c.o
[ 21%] Building CXX object lib/coraxlib/src/corax/CMakeFiles/corax_obj.dir/io/newick.cpp.o
/Users/bbraschi/Scratch/root_digger/lib/coraxlib/src/corax/io/newick.cpp:73:3: warning: 'auto' type specifier is a C++11 extension [-Wc++11-extensions]
auto s = n->next;
^
/Users/bbraschi/Scratch/root_digger/lib/coraxlib/src/corax/io/newick.cpp:77:5: warning: 'auto' type specifier is a C++11 extension [-Wc++11-extensions]
auto tmp = s->next;
^
/Users/bbraschi/Scratch/root_digger/lib/coraxlib/src/corax/io/newick.cpp:178:31: error: expected member name or ';' after declaration specifiers
_input{std::move(input)}, _current_index{0} {};
^
/Users/bbraschi/Scratch/root_digger/lib/coraxlib/src/corax/io/newick.cpp:178:13: error: expected '('
_input{std::move(input)}, _current_index{0} {};
^
/Users/bbraschi/Scratch/root_digger/lib/coraxlib/src/corax/io/newick.cpp:178:30: error: expected ';' after expression
_input{std::move(input)}, _current_index{0} {};
^
;
/Users/bbraschi/Scratch/root_digger/lib/coraxlib/src/corax/io/newick.cpp:205:5: warning: 'auto' type specifier is a C++11 extension [-Wc++11-extensions]
auto f_str = consume_value_as_string();
^
/Users/bbraschi/Scratch/root_digger/lib/coraxlib/src/corax/io/newick.cpp:210:31: error: expected '(' for function-style cast or type construction
throw std::runtime_error{std::string("Float conversion failed around")
~~~~~~~~~~~~~~~~~~^
/Users/bbraschi/Scratch/root_digger/lib/coraxlib/src/corax/io/newick.cpp:225:5: warning: 'auto' type specifier is a C++11 extension [-Wc++11-extensions]
auto ret = consume_token_pos();
^
/Users/bbraschi/Scratch/root_digger/lib/coraxlib/src/corax/io/newick.cpp:228:31: error: expected '(' for function-style cast or type construction
throw std::runtime_error{
~~~~~~~~~~~~~~~~~~^
/Users/bbraschi/Scratch/root_digger/lib/coraxlib/src/corax/io/newick.cpp:251:5: warning: 'auto' type specifier is a C++11 extension [-Wc++11-extensions]
auto start_index = _current_index;
^
/Users/bbraschi/Scratch/root_digger/lib/coraxlib/src/corax/io/newick.cpp:252:5: warning: 'auto' type specifier is a C++11 extension [-Wc++11-extensions]
auto token = consume();
^
/Users/bbraschi/Scratch/root_digger/lib/coraxlib/src/corax/io/newick.cpp:253:12: warning: generalized initializer lists are a C++11 extension [-Wc++11-extensions]
return {token, start_index};
^~~~~~~~~~~~~~~~~~~~
/Users/bbraschi/Scratch/root_digger/lib/coraxlib/src/corax/io/newick.cpp:253:12: error: non-aggregate type 'std::pair<lexeme_type_t, size_t>' (aka 'pair<lexeme_type_t, unsigned long>') cannot be initialized with an initializer list
return {token, start_index};
^~~~~~~~~~~~~~~~~~~~
/Users/bbraschi/Scratch/root_digger/lib/coraxlib/src/corax/io/newick.cpp:261:14: warning: generalized initializer lists are a C++11 extension [-Wc++11-extensions]
return {"opening square bracket"};
^~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/bbraschi/Scratch/root_digger/lib/coraxlib/src/corax/io/newick.cpp:261:14: error: non-aggregate type 'std::string' (aka 'basic_string') cannot be initialized with an initializer list
return {"opening square bracket"};
^~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/bbraschi/Scratch/root_digger/lib/coraxlib/src/corax/io/newick.cpp:263:14: warning: generalized initializer lists are a C++11 extension [-Wc++11-extensions]
return {"closing square bracket"};
^~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/bbraschi/Scratch/root_digger/lib/coraxlib/src/corax/io/newick.cpp:263:14: error: non-aggregate type 'std::string' (aka 'basic_string') cannot be initialized with an initializer list
return {"closing square bracket"};
^~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/bbraschi/Scratch/root_digger/lib/coraxlib/src/corax/io/newick.cpp:265:14: warning: generalized initializer lists are a C++11 extension [-Wc++11-extensions]
return {"opening parenthesis"};
^~~~~~~~~~~~~~~~~~~~~~~
/Users/bbraschi/Scratch/root_digger/lib/coraxlib/src/corax/io/newick.cpp:265:14: error: non-aggregate type 'std::string' (aka 'basic_string') cannot be initialized with an initializer list
return {"opening parenthesis"};
^~~~~~~~~~~~~~~~~~~~~~~
/Users/bbraschi/Scratch/root_digger/lib/coraxlib/src/corax/io/newick.cpp:267:14: warning: generalized initializer lists are a C++11 extension [-Wc++11-extensions]
return {"closing parenthesis"};
^~~~~~~~~~~~~~~~~~~~~~~
/Users/bbraschi/Scratch/root_digger/lib/coraxlib/src/corax/io/newick.cpp:267:14: error: non-aggregate type 'std::string' (aka 'basic_string') cannot be initialized with an initializer list
return {"closing parenthesis"};
^~~~~~~~~~~~~~~~~~~~~~~
/Users/bbraschi/Scratch/root_digger/lib/coraxlib/src/corax/io/newick.cpp:269:14: warning: generalized initializer lists are a C++11 extension [-Wc++11-extensions]
return {"colon"};
^~~~~~~~~
/Users/bbraschi/Scratch/root_digger/lib/coraxlib/src/corax/io/newick.cpp:269:14: error: non-aggregate type 'std::string' (aka 'basic_string') cannot be initialized with an initializer list
return {"colon"};
^~~~~~~~~
/Users/bbraschi/Scratch/root_digger/lib/coraxlib/src/corax/io/newick.cpp:271:14: warning: generalized initializer lists are a C++11 extension [-Wc++11-extensions]
return {"semicolon"};
^~~~~~~~~~~~~
/Users/bbraschi/Scratch/root_digger/lib/coraxlib/src/corax/io/newick.cpp:271:14: error: non-aggregate type 'std::string' (aka 'basic_string') cannot be initialized with an initializer list
return {"semicolon"};
^~~~~~~~~~~~~
/Users/bbraschi/Scratch/root_digger/lib/coraxlib/src/corax/io/newick.cpp:273:14: warning: generalized initializer lists are a C++11 extension [-Wc++11-extensions]
return {"comma"};
^~~~~~~~~
/Users/bbraschi/Scratch/root_digger/lib/coraxlib/src/corax/io/newick.cpp:273:14: error: non-aggregate type 'std::string' (aka 'basic_string') cannot be initialized with an initializer list
return {"comma"};
^~~~~~~~~
/Users/bbraschi/Scratch/root_digger/lib/coraxlib/src/corax/io/newick.cpp:275:14: warning: generalized initializer lists are a C++11 extension [-Wc++11-extensions]
return {"end of input"};
^~~~~~~~~~~~~~~~
/Users/bbraschi/Scratch/root_digger/lib/coraxlib/src/corax/io/newick.cpp:275:14: error: non-aggregate type 'std::string' (aka 'basic_string') cannot be initialized with an initializer list
return {"end of input"};
^~~~~~~~~~~~~~~~
/Users/bbraschi/Scratch/root_digger/lib/coraxlib/src/corax/io/newick.cpp:277:14: warning: generalized initializer lists are a C++11 extension [-Wc++11-extensions]
return {"either a identifier or a number"};
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/bbraschi/Scratch/root_digger/lib/coraxlib/src/corax/io/newick.cpp:277:14: error: non-aggregate type 'std::string' (aka 'basic_string') cannot be initialized with an initializer list
return {"either a identifier or a number"};
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/bbraschi/Scratch/root_digger/lib/coraxlib/src/corax/io/newick.cpp:279:14: warning: generalized initializer lists are a C++11 extension [-Wc++11-extensions]
return {"unknown token"};
^~~~~~~~~~~~~~~~~
/Users/bbraschi/Scratch/root_digger/lib/coraxlib/src/corax/io/newick.cpp:279:14: error: non-aggregate type 'std::string' (aka 'basic_string') cannot be initialized with an initializer list
return {"unknown token"};
^~~~~~~~~~~~~~~~~
/Users/bbraschi/Scratch/root_digger/lib/coraxlib/src/corax/io/newick.cpp:324:31: error: expected '(' for function-style cast or type construction
throw std::runtime_error{"The punctuation was unrecognized"};
~~~~~~~~~~~~~~~~~~^
/Users/bbraschi/Scratch/root_digger/lib/coraxlib/src/corax/io/newick.cpp:335:3: warning: 'auto' type specifier is a C++11 extension [-Wc++11-extensions]
auto token = peak();
^
/Users/bbraschi/Scratch/root_digger/lib/coraxlib/src/corax/io/newick.cpp:400:31: error: expected member name or ';' after declaration specifiers
_lexer{std::move(input)},
^
/Users/bbraschi/Scratch/root_digger/lib/coraxlib/src/corax/io/newick.cpp:400:13: error: expected '('
_lexer{std::move(input)},
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
18 warnings and 20 errors generated.
make[3]: *** [lib/coraxlib/src/corax/CMakeFiles/corax_obj.dir/io/newick.cpp.o] Error 1
make[2]: *** [lib/coraxlib/src/corax/CMakeFiles/corax_obj.dir/all] Error 2
make[1]: *** [all] Error 2
make: *** [release] Error 2

Hi,
I'm trying to install root_Digger but I keep getting the following error message:
CMake Error at src/CMakeLists.txt:6 (add_executable):
Target "rd" links to target "MPI::MPI_CXX" but the target was not found.
I'm not sure how to fix that. Can you please help

Thanks in advance
Suha

Dear team,

I downloaded the source code and built it using the 'cmake' command. Although the making seemed successful there were no 'rd' files inside the 'bin' directory. Could you please help?

Thank you in advance

Hi, I have a tree of approx. 5000 bacterial genomes. I created this tree using a software which returns a tree and a masked alignment. I used these files to run root digger and received the following error: terminate called after throwing an instance of 'std::runtime_error' what(): lh at root is not a number: nan. When I draw a random subsample of 100 from both the tree and the alignment, root digger completes successfully. Do you have any idea what might be causing the error and how to fix it?

Hi I'm having some problem building with cmake:

cd root_digger
mkdir build
cd build
cmake -B ~/programs/root_digger/build/ -S ~/programs/root_digger/

-- The C compiler identification is GNU 9.4.0
-- The CXX compiler identification is GNU 9.4.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found Git: /usr/bin/git (found version "2.25.1") 
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
-- Found OpenMP_C: -fopenmp (found version "4.5") 
-- Found OpenMP_CXX: -fopenmp (found version "4.5") 
-- Found OpenMP: TRUE (found version "4.5")  
CMake Error at lib/CMakeLists.txt:2 (add_subdirectory):
  The source directory

    /home/administrator/programs/root_digger/lib/coraxlib

  does not contain a CMakeLists.txt file.

Seems like a silly error but usually when I specify path to build + source folders it works.

Many thanks!

Hi,
Thanks for sharing this great software. I've installed RootDigger on Ubuntu, but I cannot run it, could you help me to solve this problem? The details as follows:

(base) geobig@geobig-PowerEdge-T640:~/Users/Softwares/root_digger/root_digger/test/data$ /home/geobig/Users/Softwares/root_digger/root_digger/bin/rd -h

/home/geobig/Users/Softwares/root_digger/root_digger/bin/rd: unrecognized option '-h'
Usage: rd [options]
Version: v0.4.0-179-g4b8357d
Application Options:
--msa [FILE]
File containing the alignment.
--tree [FILE]
File containing the tree, with branch lengths.
--partition [FILE]
Optional file containing the partition specification.
Format is the same as RAxML-NG partition file.
--exhaustive
Enable exhaustive mode. This will attempt to root a tree
at every branch, and then report the results using LWR.
--early-stop
Enable early stopping. This will cause cause the search
to terminate when the root placement is sufficently
close for 2 consecutive iterations. How close they need
to be is controled by brtol. Is enabled by default for
search mode and disabled by default for exhaustive mode.
--no-early-stop
Force disable early stop.
--seed [NUMBER]
Random seed to use. Optional
--rate-cats [NUMBER]
Number of rate categories to use for the model. Default
is 1.
--invariant-sites
Enable invariant sites. Default is off.
--min-roots [NUMBER]
Minimum number of roots to start from. Optional,
Default is 1.
--root-ratio [NUMBER]
Proportion of potential starting roots to attempt
Default is 0.01
--atol [NUMBER]
Root optmization stopping tolerance. Increase this to
improve results.Default is 1e-4
--brtol [NUMBER]
When early stop mode is enabled, this controls the
distance required to trigger. Default is 1e-12
--bfgstol [NUMBER]
Tolerance for the BFGS steps. Default is 1e-7
--factor [NUMBER]
Factor for the BFGS steps. Default is 1e4
--silent
Suppress output except for the final tree
--verbose
Increase the verbosity level. Can be repeated to
level further.
(base) geobig@geobig-PowerEdge-T640:~/Users/Softwares/root_digger/root_digger/test/data$ /home/geobig/Users/Softwares/root_digger/root_digger/bin/rd --msa /home/geobig/Users/Softwares/root_digger/root_digger/test/data/protein/140.phy --tree /home/geobig/Users/Softwares/root_digger/root_digger/test/data/tree/140.tree --no-early-stop
[0.00] Running Root Digger
[0.00] Version: v0.4.0-179-g4b8357d
[0.00] Build Commit: 4b8357d
[0.00] Build Date: 2020-02-23 13:49:04
[0.00] Started: 2020-02-24 10:20:28
[0.00] Seed: 2662287295
Segmentation fault (core dumped)

Looking forward to hearing from you.

Many thanks for developing this package!

When I try to build the container from the Dockerfile I get the following error:

...
9 | >>> COPY .git/ root_digger/.git/
...
ERROR: failed to solve: failed to compute cache key: failed to calculate checksum of ref moby::re5y43wcvwl0b85ud6u7rs4rs: "/.git": not found

Any ideas how this could be fixed?

Hi. I am trying to install Root Digger. I couldn't get it with CMake or Docker. What do you recommend trying?

(base) cristianriquelme@Cristians-MacBook-Pro ~ % cd root_digger
(base) cristianriquelme@Cristians-MacBook-Pro root_digger % make
-- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES)
-- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES)
-- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND)
-- SSE SIMD not supported -> disabling
-- AVX SIMD not supported -> disabling
-- AVX2 SIMD not supported -> disabling
-- Build type: Release
-- Building coraxlib as a static library.
-- Building documentation: OFF
-- Building tests: OFF
-- Building benchmarks: OFF
-- Building difficutly prediction: OFF
-- Enable SSE SIMD kernels: Off
-- Enable AVX SIMD kernels: Off
-- Enable AVX2 SIMD kernels: Off
Non-rev enabled
-- A cache variable, namely LAPACKE_DIR, has been set to specify the install directory of LAPACKE
-- Looking for LAPACKE_dgeqrf
-- Looking for LAPACKE_dgeqrf - not found
-- Looking for lapacke : test with lapack fails
-- Looking for lapacke -- lapacke.h not found
-- Looking for lapacke -- lib lapacke not found
CMake Error at /opt/homebrew/Cellar/cmake/3.25.3/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:230 (message):
Could NOT find LAPACKE (missing: LAPACKE_LIBRARIES LAPACKE_WORKS)
Call Stack (most recent call first):
/opt/homebrew/Cellar/cmake/3.25.3/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:600 (_FPHSA_FAILURE_MESSAGE)
lib/coraxlib/cmake/FindLAPACKE.cmake:410 (find_package_handle_standard_args)
lib/coraxlib/src/corax/CMakeLists.txt:57 (find_package)

-- Configuring incomplete, errors occurred!
See also "/Users/cristianriquelme/root_digger/build/CMakeFiles/CMakeOutput.log".
See also "/Users/cristianriquelme/root_digger/build/CMakeFiles/CMakeError.log".
make: *** [release] Error 1

Attached files:

CMakeOutput.log
CMakeError.log

Hello @josephwb, @nathanweeks

I was able to run the tool successfully, but is there any flags to be added for printing the log-likelihood values because i cant see any log-likelihood values on the terminal, all i can see is only the newick format and the inference time . is there any possible way to see the log-likelihood and also BIC values.

Best
Jose

Hiya,
I ran root digger successfully, but didn't tell it to output to a file and my tree is very big, so in the log I am missing a lot of it. So I tried to run it again with exactly the same code (but asking it to write to file). This is the error code.
[0.00] [Warning] Loading options from the checkpoint file
...
[2.24] [Warning] The number of searches is less than the number of processes. Some nodes will do no work
There was an error during processing:
Indicies were not assigned before calling optimizations functions

Best wishes,
Jamie

Hello !

I was running a dataset with correct file names , correct file location and also data inside the files . ./rd -- msa --tree and the tool shows an error " There was an error during processing , Tree file could not be parsed ". is there any way to overcome this problem. I am also attaching the error.

Thank you in advance

Hi, I tried to run the program with a fixed seed to ensure my analysis was fully reproducible. I expected that the numeric value I set with --seed would be the same as the value listed in the console output after Seed:. However, these values do not match. Should these values match? I am running root digger in a container which was built using the Dockerfile in this repo.

Hi, I tried to run the program with a fixed seed to ensure my analysis was fully reproducible. I expected that the numeric value I set with --seed would be the same as the value listed in the console output after Seed:. However, these values do not match. Should these values match? I am running root digger in a container which was built using the Dockerfile in this repo.

Dear team member,

This is the same issue I posted last month. Sorry I could not reopen it. I downloaded the source code and built it using the 'cmake' command. But I am not sure what went wrong . I don't see rd file inside the 'bin'. Could you please help? Attached is the log after running cmake. Thanks in advance.

MacBook-Pro:root_digger nivi$ cmake /Users/nivi/root_digger/
-- The C compiler identification is AppleClang 13.1.6.13160021
-- The CXX compiler identification is AppleClang 13.1.6.13160021
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found Git: /usr/bin/git (found version "2.32.0 (Apple Git-132)")
-- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES)
-- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES)
-- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND)
-- Could NOT find PkgConfig (missing: PKG_CONFIG_EXECUTABLE)
-- Found GSL: /usr/local/include (found version "2.6")
CMake Deprecation Warning at lib/pll-modules/CMakeLists.txt:1 (cmake_minimum_required):
Compatibility with CMake < 2.8.12 will be removed from a future version of
CMake.

Update the VERSION argument value or use a ... suffix to tell
CMake that the project does not need compatibility with older versions.

-- pll-modules static build enabled
CMake Deprecation Warning at lib/pll-modules/libs/libpll/CMakeLists.txt:1 (cmake_minimum_required):
Compatibility with CMake < 2.8.12 will be removed from a future version of
CMake.

Update the VERSION argument value or use a ... suffix to tell
CMake that the project does not need compatibility with older versions.

-- Found BISON: /usr/bin/bison (found version "2.3")
-- Found FLEX: /usr/bin/flex (found version "2.6.4")
-- Disable sse simd, because not supported
-- Disable avx simd, because not supported
-- Disable avx2 simd, because not supported
-- Libpll static build enabled
-- pll_static
CMake Deprecation Warning at lib/pll-modules/src/CMakeLists.txt:1 (cmake_minimum_required):
Compatibility with CMake < 2.8.12 will be removed from a future version of
CMake.

Update the VERSION argument value or use a ... suffix to tell
CMake that the project does not need compatibility with older versions.

-- Will compile pll-module optimize
-- Will compile pll-module algorithm
-- Will compile pll-module binary
-- Will compile pll-module msa
-- Will compile pll-module tree
-- Will compile pll-module util
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/nivi/root_digger

Hello,

I have installed root-digger v1.7.0-21-gdb04b97

And I performed the following attempt to root an unrooted tree:

Input:

rd --msa ar122_alignment.faa --tree ar122_iqtree.nwk --exhaustive

Output:

[0.00] [Warning] Loading options from the checkpoint file
[0.01] Running Root Digger
[0.01] Version: v1.7.0-21-gdb04b97
[0.01] Build Commit: db04b97b863868bd98b7416e732ddceb715ee682
[0.01] Build Date: 2022-04-29 08:45:10
[0.01] Started: 2022-04-29 12:22:16
[0.01] Seed: 3130080073
[0.01] Number of threads per proc: 32
[0.01] Command: /usr/local/bin/rd --msa ar122_alignment.faa --tree ar122_iqtree.nwk --exhaustive
[0.01] Please report any bugs to https://groups.google.com/forum/#!forum/raxml
There was an error during processing:
Could not parse msa file

ar122_alignment is the protein alignment downloaded from http://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v1.0/phylogenies/. Also the Newick tree format is downloaded from the same ftp webpage.

Root-Digger required a tree in newick format, and a MSA in either PHYLIP or FASTA format. I changed the extension of .faa to .fasta but the same error persists. Also I performed a conversion of faa file to Phylip format obtaining the same error.

That protein alignement .faa file is produced by GT-DB-Tk software.

If you could give me some hints about how can I adapt my MSA file (ar122_alignment.faa) to be accepted by Root-digger will be very helpful.

Thanks on advance,

Magí.

Hi, I tried to run the program with a fixed seed to ensure my analysis was fully reproducible. I expected that the numeric value I set with --seed would be the same as the value listed in the console output after Seed:. However, these values do not match. Should these values match? I am running root digger in a container which was built using the Dockerfile in this repo.

Hello @team_rootdigger

I have installed the root digger correctly as u mentioned in the github page read me . but the problem now is the tool is showing the program has been killed while running at the initial step itself. it worked with the other datasets very well.the data set i used for running is sars covid datset (9499 sequences ).

waiting for you reply