Christopher Schröder

I will rerun and pipe to /dev/null to see what happens

I used pigz to speed up the compression process. The command was ` (bwa-mem2 mem -t 88 -R '@RG\tID:1875-0_Blood\tSM:1875-0_Blood\tPL:ILLUMINA' resources/genome.fasta results/merged/1875-0_Blood_R1.fastq.gz results/merged/1875-0_Blood_R2.fastq.gz | pigz -c > 1875-0_Blood.sam.gz) 2> 1875-0_Blood.log `...

Running, but it will take a lot of time. The debug mode is very slow.

I dont even know what that means OO

here is tail -n from the debug log [1875-0_Blood.v4.tail.log](https://github.com/bwa-mem2/bwa-mem2/files/5073710/1875-0_Blood.v4.tail.log)

yes, the error remains. I had no choice and switched back to bwa mem for the project and everything was mapped and downstream analysis are currently running. The memory capacity...

I tried 16 cores with the newest commit and it worked. I increase it to 32 now.

with 32 threads a get the following error: ``` bwa-mem2: src/bwamem.cpp:904: int mem_kernel1_core(FMI_search*, const mem_opt_t*, bseq1_t*, int, mem_chain_v*, mem_seed_t*, int64_t, mem_cache*, int): Assertion `num_smem < *wsize_mem' failed. ```

I dont know the technical background but I now used -K 500000000 as parameter for a few month on 100+ whole genomes and never got this error again. So I...

@skchronicles Did it work?