broken pipeline about bwa-meth

[brentp]

Hi, here is the relevant error:

Please verify that both the operating system and the processor support Intel(R) X87, CMOV, MMX, FXSAVE, SSE, SSE2, SSE3, SSSE3, SSE4_1, SSE4_2, MOVBE, POPCNT, F16C, AVX, FMA, BMI, LZCNT and AVX2 instructions.

this means that server does not support those instructions so you cant use bwa-mem2

[WRui]

Thank you for you reply, do you have some recommendations to run the bwa-meth mem2 with an AMD EPYC(Milan 7763) processor. Here are the flags of the processor:

fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm art rep_good nopl extd_apicid eagerfpu pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand hypervisor lahf_lm cmp_legacy cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw topoext perfctr_core invpcid_single retpoline_amd ssbd ibrs ibpb stibp vmmcall fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid rdseed adx smap clflushopt clwb sha_ni xsaveopt xsavec xgetbv1 clzero xsaveerptr arat umip pku ospke vaes vpclmulqdq spec_ctrl intel_stibp arch_capabilities

[brentp]

Hi, I'm not sure what the problem is except it seems that your bwa mem2 does not work on your processor.
You could verify this by trying to run bwa-mem2 directly, outside of bwa-meth.
Either way, you could also run bwa-meth.py with the normal bwa mem.