Vasimuddin Md
Vasimuddin Md
Sorry for getting back so late. Will it possible for you to share the input data, mostly reads? I will try to reproduce it at my end.
Sharing the index is not necessary. You can share it through cloud.
The index built by bwa-mem2 is different from bwa-mem, so they are not compatible. Functionality-wise bwa-mem2 is a drop-in replacement of bwa-mem.
Let me look into this. Please share if you are getting other error messages as well.
Please try with the latest master commit and check.
I tried the same setting running bwa-mem2 in avx2 on bash shell. echo $? prints 1 as the return value for me. Moreover, if the ret value is 0 then...
Are you using the latest binaries? if yes, will it be possible for you to share a small dataset where I can reproduce this issue?
Your log shows that the issue surfaced in the first chunk of reads ("[0000][ M::kt_pipeline] read 499586 sequences (74937900 bp)..."). You should be able to reproduce the issue with these...
bwa-mem2 pre-allocates some memory upfront to be used during the execution; It does reallocation if the allocated memory falls short. Memory usage is directly proportional to the number of threads...
Right now there is no failsafe in case the available memory is insufficient. The memory requirement is proportional to the number of threads, so you can try with lesser number...