Arun Subramaniyan

Sure, I will check and push a change with different names for all the ert index files.

I think you forgot to add `-Z ` in your command line and you are still using BWA-MEM2's default index, instead of ERT. Please also check if ../Homo_sapiens_assembly38.fasta.kmer_table and ../Homo_sapiens_assembly38.fasta.mlt_table...

The time to load the ERT index may be dominating the runtime when you use a large number of threads and a relatively small dataset (~5 million read pairs). One...

Could you share your machine configuration: `cat /proc/cpuinfo` and gcc version `gcc -v` you used for compiling the code ? Perhaps, using a newer gcc version could fix the issue.

I have had trouble compiling the AVX512 code with gcc 4.8.5 as well. Could you try a newer gcc version ? You can make use of the [developer toolset](https://www.softwarecollections.org/en/scls/rhscl/devtoolset-8/) available...

Are you using the ert index? Could you please share the command line?

Thanks Brad. I think you forgot to add -Z before the index prefix in the command line. You need to use -Z to indicate that you are using the ERT...

And just to double check, can you also make sure /isilon/pm/brad-projects/TimeTrials/Index_for_ert_24MAY2021/hg19.fasta.mlt_table and /isilon/pm/brad-projects/TimeTrials/Index_for_ert_24MAY2021/hg19.fasta.kmer_table exist ?

Could you share your complete run log ? I will take a look. Thanks !

If you could redirect stderr to a file and attach it here, that will be great. ./bwa-mem2.avx512bw mem -K 100000000 -c 250 -M -t 16 -v 1 -Z /isilon /pm/brad-projects/TimeTrials/AVX512BW_ERT_INDEX/hg19.fasta...