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isovic / racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:
https://github.com/lbcb-sci/racon
MIT License
271 stars 49 forks source link

Illegal instruction error #119

Open drs357 opened 5 years ago

drs357 commented 5 years ago

Hello I tried using Racon 1.3.2 and I received the error message illegal instruction. I used bbmap to generate the sam file with merged illumina reads. If there is more information that would be helpful to provide, please let me know.

Thanks, Dave

rvaser commented 5 years ago

Hi Dave, are you using the executable from bioconda or did you make a fresh git clone and compile it manually?

Best regards, Robert

drs357 commented 5 years ago

I am using it from bioconda

rvaser commented 5 years ago

Run grep "sse" /proc/cpuinfo and check whether there is sse4.1 listed.

drs357 commented 5 years ago

This is what comes back when I run that command: 

rity ept vpid ibpb ibrs stibp ssbd
flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt aes lahf_lm ida arat dtherm pti retpoline tpr_shadow vnmi flexpriority ept vpid ibpb ibrs stibp ssbd
flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt aes lahf_lm ida arat dtherm pti retpoline tpr_shadow vnmi flexpriority ept vpid ibpb ibrs stibp ssbd
flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt aes lahf_lm ida arat dtherm pti retpoline tpr_shadow vnmi flexpriority ept vpid ibpb ibrs stibp ssbd
flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt aes lahf_lm ida arat dtherm pti retpoline tpr_shadow vnmi flexpriority ept vpid ibpb ibrs stibp ssbd
flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt aes lahf_lm ida arat dtherm pti retpoline tpr_shadow vnmi flexpriority ept vpid ibpb ibrs stibp ssbd
flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt aes lahf_lm ida arat dtherm pti retpoline tpr_shadow vnmi flexpriority ept vpid ibpb ibrs stibp ssbd
flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt aes lahf_lm ida arat dtherm pti retpoline tpr_shadow vnmi flexpriority ept vpid ibpb ibrs stibp ssbd
flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt aes lahf_lm ida arat dtherm pti retpoline tpr_shadow vnmi flexpriority ept vpid ibpb ibrs stibp ssbd
flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt aes lahf_lm ida arat dtherm pti retpoline tpr_shadow vnmi flexpriority ept vpid ibpb ibrs stibp ssbd
flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt aes lahf_lm ida arat dtherm pti retpoline tpr_shadow vnmi flexpriority ept vpid ibpb ibrs stibp ssbd
flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt aes lahf_lm ida arat dtherm pti retpoline tpr_shadow vnmi flexpriority ept vpid ibpb ibrs stibp ssbd
flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt aes lahf_lm ida arat dtherm pti retpoline tpr_shadow vnmi flexpriority ept vpid ibpb ibrs stibp ssbd
flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt aes lahf_lm ida arat dtherm pti retpoline tpr_shadow vnmi flexpriority ept vpid ibpb ibrs stibp ssbd
flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt aes lahf_lm ida arat dtherm pti retpoline tpr_shadow vnmi flexpriority ept vpid ibpb ibrs stibp ssbd
flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt aes lahf_lm ida arat dtherm pti retpoline tpr_shadow vnmi flexpriority ept vpid ibpb ibrs stibp ssbd
flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt aes lahf_lm ida arat dtherm pti retpoline tpr_shadow vnmi flexpriority ept vpid ibpb ibrs stibp ssbd
flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt aes lahf_lm ida arat dtherm pti retpoline tpr_shadow vnmi flexpriority ept vpid ibpb ibrs stibp ssbd
flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt aes lahf_lm ida arat dtherm pti retpoline tpr_shadow vnmi flexpriority ept vpid ibpb ibrs stibp ssbd
flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt aes lahf_lm ida arat dtherm pti retpoline tpr_shadow vnmi flexpriority ept vpid ibpb ibrs stibp ssbd
flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt aes lahf_lm ida arat dtherm pti retpoline tpr_shadow vnmi flexpriority ept vpid ibpb ibrs stibp ssbd
flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt aes lahf_lm ida arat dtherm pti retpoline tpr_shadow vnmi flexpriority ept vpid ibpb ibrs stibp ssbd
rvaser commented 5 years ago

Looks fine. Can you try git clone and compiling manually? I do not know what could be the problem at the moment.

drs357 commented 5 years ago

I have never compiled manually, could there potentially be a problem with any of my input files?

rvaser commented 5 years ago

The conda version worked for you with different input data?

drs357 commented 5 years ago

No this is my first time trying it. When using git clone what would the command be?

rvaser commented 5 years ago

Run the following:

git clone --recursive https://github.com/isovic/racon
cd racon
mkdir build
cd build
cmake -DCMAKE_BUILD_TYPE=Release -Dracon_build_tests=ON ..
make

You will get the executables in racon/build/bin. Try running racon_test to see if everything works now.

drs357 commented 5 years ago

I got an error when running the first command:

CMake Error at CMakeLists.txt:1 (cmake_minimum_required):
  CMake 3.2 or higher is required.  You are running version 2.6.4

-- Configuring incomplete, errors occurred!
rvaser commented 5 years ago

Ugh, which OS do you have?

drs357 commented 5 years ago 
(assembly) [drs4001@hippocampus build]$ lsb_release -a
LSB Version:    :core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch
Distributor ID: RedHatEnterpriseServer
Description:    Red Hat Enterprise Linux Server release 6.3 (Santiago)
Release:        6.3
Codename:       Santiago
drs357 commented 5 years ago

Sorry I am pretty poor with command-line/computer things

rvaser commented 5 years ago

No problem:) Try to follow this http://jotmynotes.blogspot.com/2016/10/updating-cmake-from-2811-to-362-or.html.

drs357 commented 5 years ago

I do not have authorization to use sudo on the server

drs357 commented 5 years ago

Is there anyway to update it through conda?

rvaser commented 5 years ago

Well I am not sure what is the actual problem with the conda executable. Could you try not removing the old cmake and run the installation lines without sudo? I guess it should work.

drs357 commented 5 years ago

So the anoconda library it is only version 3.14. I uninstalled the current cmake, do I just use wget to install the newest one?

rvaser commented 5 years ago 
wget https://cmake.org/files/v3.6/cmake-3.6.2.tar.gz
tar -zxvf cmake-3.6.2.tar.gz
cd cmake-3.6.2
sudo ./bootstrap --prefix=/usr/local
sudo make
sudo make install
drs357 commented 5 years ago

I am a little confused with the last part

and edit ~/.bash_profile to PATH=/usr/local/bin:$PATH:$HOME/bin.

drs357 commented 5 years ago

Also I cannot use sudo for those parts of the command

rvaser commented 5 years ago

Try without sudo, do not edit bash_profile, after installation try to run the new cmake directly.

drs357 commented 5 years ago

So the first 3 parts worked, I am in the cmake directory, but if I hit cmake -h I get this:

cmake version 2.6-patch 4
Usage

  cmake [options] <path-to-source>
  cmake [options] <path-to-existing-build>

Again thanks for your patience, I am really new to command line. It looks like it is still using an old version of cmake

rvaser commented 5 years ago

Try running ./cmake -h from the directory (if you leave out the dot it will run the one in /usr/bin or wherever it is).

drs357 commented 5 years ago

When I do it like that, I get no such file or directory found

drs357 commented 5 years ago

when downloading from conda-forge, bioconda, or anaconda cloud, it is not possible to select which version, correct?

rvaser commented 5 years ago

Can you print the contents of the cmake directory in which you are currently? I am not sure if you can select different versions from bioconda.

drs357 commented 5 years ago 
Auxiliary         CMakeCPackOptions.cmake.in  CMakeLogo.gif             configure         CTestConfig.cmake     doxygen.config  Modules     Source     Utilities
bootstrap         CMakeGraphVizOptions.cmake  cmake_uninstall.cmake.in  CONTRIBUTING.rst  CTestCustom.cmake.in  Help            Packaging   Templates
CMakeCPack.cmake  CMakeLists.txt              CompileFlags.cmake        Copyright.txt     DartConfig.cmake      Licenses        README.rst  Tests
rvaser commented 5 years ago

I have locally done the following:

wget https://cmake.org/files/v3.6/cmake-3.6.2.tar.gz
tar -zxvf cmake-3.6.2.tar.gz
cd cmake-3.6.2
./bootstrap
make

which creates a cmake-3.6.2/bin/cmake. I do not see the bin directory at your side.

Try removing --prefix=/usr/local part from bootstrap command.

drs357 commented 5 years ago

Likely because I did it originally with the sudo in front of make, I re-did the command you posted and it is still running.

drs357 commented 5 years ago

okay it just completed saying cmake has bootstrapped now run gmake. This is in the directory:

Auxiliary       CMakeCPack.cmake                   CMakeGraphVizOptions.cmake  cmake_uninstall.cmake     Copyright.txt            CTestCustom.cmake.in   doxygen.config  Packaging   Tests
bin             CMakeCPackOptions.cmake            cmake_install.cmake         cmake_uninstall.cmake.in  CPackConfig.cmake        CTestScript.cmake      Help            README.rst  Utilities
bootstrap       CMakeCPackOptions.cmake.in         CMakeLists.txt              CompileFlags.cmake        CPackSourceConfig.cmake  CTestTestfile.cmake    Licenses        Source
Bootstrap.cmk   CMake.Documentation.SphinxHTML.qs  CMakeLogo.gif               configure                 CTestConfig.cmake        DartConfig.cmake       Makefile        Templates
CMakeCache.txt  CMakeFiles                         CMake.qs                    CONTRIBUTING.rst          CTestCustom.cmake        DartConfiguration.tcl  Modules         Testing
rvaser commented 5 years ago

Try running ./bin/cmake --version.

drs357 commented 5 years ago

When I run that, still get no file or directory....sorry for all the trouble

rvaser commented 5 years ago

Did you run gmake?

drs357 commented 5 years ago

nope, probably why, doing that right now

drs357 commented 5 years ago

okay so now after running gmake, ./bin/cmake --version shows the proper version

rvaser commented 5 years ago

Finally :D Now go back to racon/build folder and run <path_to_freshly_installed_cmake_directory>/bin/cmake -DCMAKE_BUILD_TYPE=Release -Dracon_build_tests=ON ...

drs357 commented 5 years ago

okay so I did that, got this: 

(assembly) [drs4001@hippocampus build]$ /athena/masonlab/scratch/projects/metagenomics/vartanian_lab_ms_study/analysis/cmake-3.6.2/bin/cmake -DCMAKE_BUILD_TYPE=Release -Dracon_build_tests=ON ..
-- The C compiler identification is GNU 4.4.7
-- The CXX compiler identification is GNU 4.4.7
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of off64_t
-- Check size of off64_t - done
-- Looking for fseeko
-- Looking for fseeko - found
-- Looking for unistd.h
-- Looking for unistd.h - found
-- Renaming
--     /athena/masonlab/scratch/projects/metagenomics/vartanian_lab_ms_study/analysis/racon/vendor/bioparser/vendor/zlib/zconf.h
-- to 'zconf.h.included' because this file is included with zlib
-- but CMake generates it automatically in the build directory.
Setting warning flags
-- Found PythonInterp: /home/drs4001/miniconda3/envs/assembly/bin/python (found version "3.6.8")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Check if compiler accepts -pthread
-- Check if compiler accepts -pthread - yes
-- Found Threads: TRUE
-- Configuring done
-- Generating done
-- Build files have been written to: /athena/masonlab/scratch/projects/metagenomics/vartanian_lab_ms_study/analysis/racon/build
rvaser commented 5 years ago

Now run make (or gmake) which will create racon and racon_test in racon/build. Then run ./bin/racon_test to see if it works.

drs357 commented 5 years ago

when running make I get an error :(

(assembly) [drs4001@hippocampus build]$ gmake
[  2%] Building CXX object vendor/googletest/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o
cc1plus: warnings being treated as errors
In file included from /athena/masonlab/scratch/projects/metagenomics/vartanian_lab_ms_study/analysis/racon/vendor/googletest/googletest/include/gtest/gtest.h:58,
                 from /athena/masonlab/scratch/projects/metagenomics/vartanian_lab_ms_study/analysis/racon/vendor/googletest/googletest/src/gtest-all.cc:39:
/athena/masonlab/scratch/projects/metagenomics/vartanian_lab_ms_study/analysis/racon/vendor/googletest/googletest/include/gtest/internal/gtest-internal.h:1078: error: comma at end of enumerator list
In file included from /athena/masonlab/scratch/projects/metagenomics/vartanian_lab_ms_study/analysis/racon/vendor/googletest/googletest/include/gtest/internal/gtest-param-util.h:47,
                 from /athena/masonlab/scratch/projects/metagenomics/vartanian_lab_ms_study/analysis/racon/vendor/googletest/googletest/include/gtest/gtest-param-test.h:190,
                 from /athena/masonlab/scratch/projects/metagenomics/vartanian_lab_ms_study/analysis/racon/vendor/googletest/googletest/include/gtest/gtest.h:62,
                 from /athena/masonlab/scratch/projects/metagenomics/vartanian_lab_ms_study/analysis/racon/vendor/googletest/googletest/src/gtest-all.cc:39:
/athena/masonlab/scratch/projects/metagenomics/vartanian_lab_ms_study/analysis/racon/vendor/googletest/googletest/include/gtest/gtest-printers.h:407: error: comma at end of enumerator list
gmake[2]: *** [vendor/googletest/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o] Error 1
gmake[1]: *** [vendor/googletest/googletest/CMakeFiles/gtest.dir/all] Error 2
gmake: *** [all] Error 2
rvaser commented 5 years ago

Ugh, add -Wno-error at the end of string at line 8 in racon/CMakeLists.txt. Run cmake and make again from the build directory.

If that does not work again, delete the contents of the build directory and run cmake without -Dracon_build_tests=ON. I'll get back to you in the morning.

drs357 commented 5 years ago

just to make sure this is correct, this is how I do line 8:

set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -pedantic") -Wno-error

rvaser commented 5 years ago

Line 8 should look like this: set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -pedantic -Wno-error")

drs357 commented 5 years ago

Fixing the cmakelist file allowed it to configure, but ./bin/racon_test still doesn't work

rvaser commented 5 years ago

Did you run gmake/make afterwards? Is the ./bin directory empty?

drs357 commented 5 years ago

with doing option 1, i still get the same error after hitting make 

(assembly) [drs4001@hippocampus build]$ make
[  2%] Building CXX object vendor/googletest/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o
cc1plus: warnings being treated as errors
In file included from /athena/masonlab/scratch/projects/metagenomics/vartanian_lab_ms_study/analysis/racon/vendor/googletest/googletest/include/gtest/gtest.h:58,
                 from /athena/masonlab/scratch/projects/metagenomics/vartanian_lab_ms_study/analysis/racon/vendor/googletest/googletest/src/gtest-all.cc:39:
/athena/masonlab/scratch/projects/metagenomics/vartanian_lab_ms_study/analysis/racon/vendor/googletest/googletest/include/gtest/internal/gtest-internal.h:1078: error: comma at end of enumerator list
In file included from /athena/masonlab/scratch/projects/metagenomics/vartanian_lab_ms_study/analysis/racon/vendor/googletest/googletest/include/gtest/internal/gtest-param-util.h:47,
                 from /athena/masonlab/scratch/projects/metagenomics/vartanian_lab_ms_study/analysis/racon/vendor/googletest/googletest/include/gtest/gtest-param-test.h:190,
                 from /athena/masonlab/scratch/projects/metagenomics/vartanian_lab_ms_study/analysis/racon/vendor/googletest/googletest/include/gtest/gtest.h:62,
                 from /athena/masonlab/scratch/projects/metagenomics/vartanian_lab_ms_study/analysis/racon/vendor/googletest/googletest/src/gtest-all.cc:39:
/athena/masonlab/scratch/projects/metagenomics/vartanian_lab_ms_study/analysis/racon/vendor/googletest/googletest/include/gtest/gtest-printers.h:407: error: comma at end of enumerator list
make[2]: *** [vendor/googletest/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o] Error 1
make[1]: *** [vendor/googletest/googletest/CMakeFiles/gtest.dir/all] Error 2
make: *** [all] Error 2
drs357 commented 5 years ago

yes the bin directory is empty

drs357 commented 5 years ago

when I also run it without -Dracon_build_tests=ON and do make, it still gives me an error

rvaser commented 5 years ago

Is it the same error? Did you clean the racon/build directory?

drs357 commented 5 years ago

I deleted the files and folders in the build directory. This is the error:

Scanning dependencies of target edlib_static
[  3%] Building CXX object vendor/edlib/CMakeFiles/edlib_static.dir/edlib/src/edlib.cpp.o
[  6%] Linking CXX static library ../../lib/libedlib_static.a
[  6%] Built target edlib_static
Scanning dependencies of target zlibstatic
[  9%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/adler32.o
[ 12%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/compress.o
[ 16%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/crc32.o
[ 19%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/deflate.o
[ 22%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/gzclose.o
[ 25%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/gzlib.o
[ 29%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/gzread.o
[ 32%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/gzwrite.o
[ 35%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/inflate.o
[ 38%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/infback.o
[ 41%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/inftrees.o
[ 45%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/inffast.o
[ 48%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/trees.o
[ 51%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/uncompr.o
[ 54%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/zutil.o
[ 58%] Linking C static library ../../lib/libz.a
[ 58%] Built target zlibstatic
Scanning dependencies of target spoa
[ 61%] Building CXX object vendor/spoa/CMakeFiles/spoa.dir/src/alignment_engine.cpp.o
In file included from /athena/masonlab/scratch/projects/metagenomics/vartanian_lab_ms_study/analysis/racon/vendor/spoa/src/sisd_alignment_engine.hpp:15,
                 from /athena/masonlab/scratch/projects/metagenomics/vartanian_lab_ms_study/analysis/racon/vendor/spoa/src/alignment_engine.cpp:11:
/athena/masonlab/scratch/projects/metagenomics/vartanian_lab_ms_study/analysis/racon/vendor/spoa/include/spoa/alignment_engine.hpp:24: error: expected nested-name-specifier before ‘Alignment’
/athena/masonlab/scratch/projects/metagenomics/vartanian_lab_ms_study/analysis/racon/vendor/spoa/include/spoa/alignment_engine.hpp:24: error: ‘Alignment’ has not been declared
/athena/masonlab/scratch/projects/metagenomics/vartanian_lab_ms_study/analysis/racon/vendor/spoa/include/spoa/alignment_engine.hpp:24: error: expected ‘;’ before ‘=’ token
/athena/masonlab/scratch/projects/metagenomics/vartanian_lab_ms_study/analysis/racon/vendor/spoa/include/spoa/alignment_engine.hpp:24: error: expected unqualified-id before ‘=’ token
/athena/masonlab/scratch/projects/metagenomics/vartanian_lab_ms_study/analysis/racon/vendor/spoa/include/spoa/alignment_engine.hpp:36: error: ‘Alignment’ does not name a type
/athena/masonlab/scratch/projects/metagenomics/vartanian_lab_ms_study/analysis/racon/vendor/spoa/include/spoa/alignment_engine.hpp:39: error: ‘Alignment’ does not name a type
In file included from /athena/masonlab/scratch/projects/metagenomics/vartanian_lab_ms_study/analysis/racon/vendor/spoa/src/alignment_engine.cpp:11:
/athena/masonlab/scratch/projects/metagenomics/vartanian_lab_ms_study/analysis/racon/vendor/spoa/src/sisd_alignment_engine.hpp:29: error: expected ‘;’ before ‘override’
/athena/masonlab/scratch/projects/metagenomics/vartanian_lab_ms_study/analysis/racon/vendor/spoa/src/sisd_alignment_engine.hpp:31: error: ‘Alignment’ does not name a type
/athena/masonlab/scratch/projects/metagenomics/vartanian_lab_ms_study/analysis/racon/vendor/spoa/src/sisd_alignment_engine.hpp:42: error: ‘Alignment’ does not name a type
/athena/masonlab/scratch/projects/metagenomics/vartanian_lab_ms_study/analysis/racon/vendor/spoa/src/sisd_alignment_engine.hpp:49: error: expected ‘;’ before ‘noexcept’
In file included from /athena/masonlab/scratch/projects/metagenomics/vartanian_lab_ms_study/analysis/racon/vendor/spoa/src/alignment_engine.cpp:12:
/athena/masonlab/scratch/projects/metagenomics/vartanian_lab_ms_study/analysis/racon/vendor/spoa/src/simd_alignment_engine.hpp:29: error: expected ‘;’ before ‘override’
/athena/masonlab/scratch/projects/metagenomics/vartanian_lab_ms_study/analysis/racon/vendor/spoa/src/simd_alignment_engine.hpp:31: error: ‘Alignment’ does not name a type
/athena/masonlab/scratch/projects/metagenomics/vartanian_lab_ms_study/analysis/racon/vendor/spoa/src/simd_alignment_engine.hpp:43: error: expected constructor, destructor, or type conversion before ‘align’
/athena/masonlab/scratch/projects/metagenomics/vartanian_lab_ms_study/analysis/racon/vendor/spoa/src/simd_alignment_engine.hpp:52: error: expected initializer before ‘noexcept’
/athena/masonlab/scratch/projects/metagenomics/vartanian_lab_ms_study/analysis/racon/vendor/spoa/src/alignment_engine.cpp: In function ‘std::unique_ptr<spoa::AlignmentEngine, std::default_delete<spoa::AlignmentEngine> > spoa::createAlignmentEngine(spoa::AlignmentType, int8_t, int8_t, int8_t)’:
/athena/masonlab/scratch/projects/metagenomics/vartanian_lab_ms_study/analysis/racon/vendor/spoa/src/alignment_engine.cpp:39: error: ‘nullptr’ was not declared in this scope
/athena/masonlab/scratch/projects/metagenomics/vartanian_lab_ms_study/analysis/racon/vendor/spoa/src/alignment_engine.cpp: At global scope:
/athena/masonlab/scratch/projects/metagenomics/vartanian_lab_ms_study/analysis/racon/vendor/spoa/src/alignment_engine.cpp:52: error: ‘Alignment’ does not name a type
make[2]: *** [vendor/spoa/CMakeFiles/spoa.dir/src/alignment_engine.cpp.o] Error 1
make[1]: *** [vendor/spoa/CMakeFiles/spoa.dir/all] Error 2