line 16: 95164 Illegal instruction

[KylonisThanos]

I have installed medaka 1.8.1 in a conda environment , Ubuntu 20.04 LTS virtual box i wrote a python script that activates the environment so i can run the medaka program (it is part of a bigger workflow ) // import subprocess import os

def activate_conda_environment(env_name): subprocess.run(['/home/thanos/anaconda3/bin/conda run ', '/home/thanos/anaconda3/bin/activate', env_name], shell=True)

def deactivate_conda_environment(): subprocess.run(['/home/thanos/anaconda3/bin/conda run', '/home/thanos/anaconda3/bin/deactivate'], shell=True)

activate_conda_environment('med')

subprocess.run(['fastqc', '/home/thanos/genome_assembly/nanopore_data.fastq'])

Run Medaka

subprocess.run([ '/home/thanos/.local/bin/medaka_consensus' , '-i' , '/home/thanos/genome_assembly/porechop_output/trimmed.fastq' , '-d' , '/home/thanos/genome_assembly/flye_output/assembly.fasta' ,'-o' , '/home/thanos/genome_assembly/medaka_output'] , shell=True)

deactivate_conda_environment() //

and i got this error message on my terminal like for 3 days. "(med) thanos@thanos:~/genome_assembly$ python3 medaka_script.py /home/thanos/.local/bin/medaka_consensus: line 16: 95164 Illegal instruction (core dumped) medaka tools list_models /home/thanos/.local/bin/medaka_consensus: line 25: python: command not found (med) thanos@thanos:~/genome_assembly$ "

about my CPU

(base) thanos@thanos:~$ cat /proc/cpuinfo processor : 0 vendor_id : GenuineIntel cpu family : 6 model : 167 model name : 11th Gen Intel(R) Core(TM) i7-11700K @ 3.60GHz stepping : 1 microcode : 0xffffffff cpu MHz : 3599.996 cache size : 16384 KB physical id : 0 siblings : 8 core id : 0 cpu cores : 8 apicid : 0 initial apicid : 0 fpu : yes fpu_exception : yes cpuid level : 22 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx rdtscp lm constant_tsc rep_good nopl xtopology nonstop_tsc cpuid tsc_known_freq pni pclmulqdq ssse3 cx16 pcid sse4_1 sse4_2 movbe popcnt aes rdrand hypervisor lahf_lm abm 3dnowprefetch invpcid_single ibrs_enhanced fsgsbase bmi1 bmi2 invpcid rdseed clflushopt md_clear flush_l1d arch_capabilities bugs : spectre_v1 spectre_v2 spec_store_bypass swapgs mmio_stale_data retbleed eibrs_pbrsb bogomips : 7199.99 clflush size : 64 cache_alignment : 64 address sizes : 39 bits physical, 48 bits virtual power management:

processor : 1 vendor_id : GenuineIntel cpu family : 6 model : 167 model name : 11th Gen Intel(R) Core(TM) i7-11700K @ 3.60GHz stepping : 1 microcode : 0xffffffff cpu MHz : 3599.996 cache size : 16384 KB physical id : 0 siblings : 8 core id : 1 cpu cores : 8 apicid : 1 initial apicid : 1 fpu : yes fpu_exception : yes cpuid level : 22 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx rdtscp lm constant_tsc rep_good nopl xtopology nonstop_tsc cpuid tsc_known_freq pni pclmulqdq ssse3 cx16 pcid sse4_1 sse4_2 movbe popcnt aes rdrand hypervisor lahf_lm abm 3dnowprefetch invpcid_single ibrs_enhanced fsgsbase bmi1 bmi2 invpcid rdseed clflushopt md_clear flush_l1d arch_capabilities bugs : spectre_v1 spectre_v2 spec_store_bypass swapgs mmio_stale_data retbleed eibrs_pbrsb bogomips : 7199.99 clflush size : 64 cache_alignment : 64 address sizes : 39 bits physical, 48 bits virtual power management:

processor : 2 vendor_id : GenuineIntel cpu family : 6 model : 167 model name : 11th Gen Intel(R) Core(TM) i7-11700K @ 3.60GHz stepping : 1 microcode : 0xffffffff cpu MHz : 3599.996 cache size : 16384 KB physical id : 0 siblings : 8 core id : 2 cpu cores : 8 apicid : 2 initial apicid : 2 fpu : yes fpu_exception : yes cpuid level : 22 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx rdtscp lm constant_tsc rep_good nopl xtopology nonstop_tsc cpuid tsc_known_freq pni pclmulqdq ssse3 cx16 pcid sse4_1 sse4_2 movbe popcnt aes rdrand hypervisor lahf_lm abm 3dnowprefetch invpcid_single ibrs_enhanced fsgsbase bmi1 bmi2 invpcid rdseed clflushopt md_clear flush_l1d arch_capabilities bugs : spectre_v1 spectre_v2 spec_store_bypass swapgs mmio_stale_data retbleed eibrs_pbrsb bogomips : 7199.99 clflush size : 64 cache_alignment : 64 address sizes : 39 bits physical, 48 bits virtual power management:

processor : 3 vendor_id : GenuineIntel cpu family : 6 model : 167 model name : 11th Gen Intel(R) Core(TM) i7-11700K @ 3.60GHz stepping : 1 microcode : 0xffffffff cpu MHz : 3599.996 cache size : 16384 KB physical id : 0 siblings : 8 core id : 3 cpu cores : 8 apicid : 3 initial apicid : 3 fpu : yes fpu_exception : yes cpuid level : 22 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx rdtscp lm constant_tsc rep_good nopl xtopology nonstop_tsc cpuid tsc_known_freq pni pclmulqdq ssse3 cx16 pcid sse4_1 sse4_2 movbe popcnt aes rdrand hypervisor lahf_lm abm 3dnowprefetch invpcid_single ibrs_enhanced fsgsbase bmi1 bmi2 invpcid rdseed clflushopt md_clear flush_l1d arch_capabilities bugs : spectre_v1 spectre_v2 spec_store_bypass swapgs mmio_stale_data retbleed eibrs_pbrsb bogomips : 7199.99 clflush size : 64 cache_alignment : 64 address sizes : 39 bits physical, 48 bits virtual power management:

processor : 4 vendor_id : GenuineIntel cpu family : 6 model : 167 model name : 11th Gen Intel(R) Core(TM) i7-11700K @ 3.60GHz stepping : 1 microcode : 0xffffffff cpu MHz : 3599.996 cache size : 16384 KB physical id : 0 siblings : 8 core id : 4 cpu cores : 8 apicid : 4 initial apicid : 4 fpu : yes fpu_exception : yes cpuid level : 22 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx rdtscp lm constant_tsc rep_good nopl xtopology nonstop_tsc cpuid tsc_known_freq pni pclmulqdq ssse3 cx16 pcid sse4_1 sse4_2 movbe popcnt aes rdrand hypervisor lahf_lm abm 3dnowprefetch invpcid_single ibrs_enhanced fsgsbase bmi1 bmi2 invpcid rdseed clflushopt md_clear flush_l1d arch_capabilities bugs : spectre_v1 spectre_v2 spec_store_bypass swapgs mmio_stale_data retbleed eibrs_pbrsb bogomips : 7199.99 clflush size : 64 cache_alignment : 64 address sizes : 39 bits physical, 48 bits virtual power management:

processor : 5 vendor_id : GenuineIntel cpu family : 6 model : 167 model name : 11th Gen Intel(R) Core(TM) i7-11700K @ 3.60GHz stepping : 1 microcode : 0xffffffff cpu MHz : 3599.996 cache size : 16384 KB physical id : 0 siblings : 8 core id : 5 cpu cores : 8 apicid : 5 initial apicid : 5 fpu : yes fpu_exception : yes cpuid level : 22 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx rdtscp lm constant_tsc rep_good nopl xtopology nonstop_tsc cpuid tsc_known_freq pni pclmulqdq ssse3 cx16 pcid sse4_1 sse4_2 movbe popcnt aes rdrand hypervisor lahf_lm abm 3dnowprefetch invpcid_single ibrs_enhanced fsgsbase bmi1 bmi2 invpcid rdseed clflushopt md_clear flush_l1d arch_capabilities bugs : spectre_v1 spectre_v2 spec_store_bypass swapgs mmio_stale_data retbleed eibrs_pbrsb bogomips : 7199.99 clflush size : 64 cache_alignment : 64 address sizes : 39 bits physical, 48 bits virtual power management:

processor : 6 vendor_id : GenuineIntel cpu family : 6 model : 167 model name : 11th Gen Intel(R) Core(TM) i7-11700K @ 3.60GHz stepping : 1 microcode : 0xffffffff cpu MHz : 3599.996 cache size : 16384 KB physical id : 0 siblings : 8 core id : 6 cpu cores : 8 apicid : 6 initial apicid : 6 fpu : yes fpu_exception : yes cpuid level : 22 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx rdtscp lm constant_tsc rep_good nopl xtopology nonstop_tsc cpuid tsc_known_freq pni pclmulqdq ssse3 cx16 pcid sse4_1 sse4_2 movbe popcnt aes rdrand hypervisor lahf_lm abm 3dnowprefetch invpcid_single ibrs_enhanced fsgsbase bmi1 bmi2 invpcid rdseed clflushopt md_clear flush_l1d arch_capabilities bugs : spectre_v1 spectre_v2 spec_store_bypass swapgs mmio_stale_data retbleed eibrs_pbrsb bogomips : 7199.99 clflush size : 64 cache_alignment : 64 address sizes : 39 bits physical, 48 bits virtual power management:

processor : 7 vendor_id : GenuineIntel cpu family : 6 model : 167 model name : 11th Gen Intel(R) Core(TM) i7-11700K @ 3.60GHz stepping : 1 microcode : 0xffffffff cpu MHz : 3599.996 cache size : 16384 KB physical id : 0 siblings : 8 core id : 7 cpu cores : 8 apicid : 7 initial apicid : 7 fpu : yes fpu_exception : yes cpuid level : 22 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx rdtscp lm constant_tsc rep_good nopl xtopology nonstop_tsc cpuid tsc_known_freq pni pclmulqdq ssse3 cx16 pcid sse4_1 sse4_2 movbe popcnt aes rdrand hypervisor lahf_lm abm 3dnowprefetch invpcid_single ibrs_enhanced fsgsbase bmi1 bmi2 invpcid rdseed clflushopt md_clear flush_l1d arch_capabilities bugs : spectre_v1 spectre_v2 spec_store_bypass swapgs mmio_stale_data retbleed eibrs_pbrsb bogomips : 7199.99 clflush size : 64 cache_alignment : 64 address sizes : 39 bits physical, 48 bits virtual power management:

[cjw85]

We are not responsible for the compilation of the packages on conda. You should take this up with the bioconda maintainers.

[KylonisThanos]

We are not responsible for the compilation of the packages on conda. You should take this up with the bioconda maintainers.

I would appreciate the slightest idea of how can i solve this problem , since i am just a biologist an not a computer engineer or a developer. I cant even clarify what the problem is .

[cjw85]

You may try installing using the PyPI package as documented in the README file.

The issue here likely stems from the fact you are running on a Virtual Machine. Your virtual machine appears not to support all the processor instructions that the bioconda package is trying to use. I would suggest not using a virtual machine.

[cjw85]

Closing through lack of response.