Open sen1019san opened 3 years ago
That is an older version with known issues. Please retry with the current version 2-2.1. You will need to rebuild the indexes. The memory requirement will be far lower as will index loading time.
This may not resolve the issue but it will be far easier to diagnose the problem on the current version.
Why not use minimap2 as opposed to bwa mem1 or 2 for aligning nanopore data ?
Hi, I am trying to align 16S/ITS read from nanopore sequencing against 16S/ITS reference. bwa-mem2 (v2.0pre2) do well in building index. But it fails in the alignment step. bwa-mem2 version: 2.0pre2_x64-linux os: Ubuntu 16.04.7 LTS cpu: Intel(R) Xeon(R) CPU E7-8867 v4 @ 2.40GHz ram: 503GB The reference genome size is 320Mb, and the read file size is 14Mb with 10000 reads.
Here shows the command.
The error information shows as follows.
The How can I solve this problem? Any advice would be appreciated.