Illegal instruction error

[drs357]

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]

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]

I am using it from bioconda

[rvaser]

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

[drs357]

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]

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

[drs357]

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

[rvaser]

The conda version worked for you with different input data?

[drs357]

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

[rvaser]

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]

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]

Ugh, which OS do you have?

[drs357]

(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]

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

[rvaser]

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

[drs357]

I do not have authorization to use sudo on the server

[drs357]

Is there anyway to update it through conda?

[rvaser]

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]

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]

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]

I am a little confused with the last part

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

[drs357]

Also I cannot use sudo for those parts of the command

[rvaser]

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

[drs357]

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]

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]

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

[drs357]

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

[rvaser]

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]

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]

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]

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.