Snakemake-Aligment using BWA-MEM2

Hello

I have started using snakemake 6.5.2 to align fastq files with reference file. I have pasted the error below in this question. How to allocate memory in the snakefile and read the header from samfile, ‘-‘. This is the snakefile (wrapper for running alignment):

  rule bwa_mem2_mem:
        input:
            reads=["/scicore/home/cichon/GROUP/test_workflow/samples/{sample}.1.fq", "/scicore/home/cichon/GROUP/test_workflow/samples/{sample}.2.fq"]
        output:
            "/scicore/home/cichon/GROUP/test_workflow/output/{sample}.bam"
        log:
            "/scicore/home/cichon/GROUP/test_workflow/output/{sample}.log"
        params:
            index="/scicore/home/cichon/GROUP/test_workflow/data/gch38.fa",
            extra=r"-R '@RGtID:{sample}tSM:{sample}'",
            sort="none",             # Can be 'none', 'samtools' or 'picard'.
            sort_order="coordinate", # Can be 'coordinate' (default) or 'queryname'.
            sort_extra=""     

        threads: 8
        wrapper:
            "0.77.0/bio/bwa-mem2/mem"

I used this command to execute the above snakemake file:

snakemake –use-conda –snakefile Snakefile –cores -p /scicore/home/cichon/GROUP/test_workflow/output/DE98NGSUKBD117612_1.bam /scicore/home/cichon/GROUP/test_workflow/output/DE71NGSUKBD117613_3.bam

Error from log file:

Looking to launch executable "/scicore/home/cichon/GROUP/test_workflow/.snakemake/conda/0ecf6ba401c70d7501c73bb1c733a060/bin/bwa-mem2.avx", simd = .avx
Launching executable "/scicore/home/cichon/GROUP/test_workflow/.snakemake/conda/0ecf6ba401c70d7501c73bb1c733a060/bin/bwa-mem2.avx"
-----------------------------
Executing in AVX mode!!
-----------------------------
* SA compression enabled with xfactor: 8
* Ref file: /scicore/home/cichon/GROUP/test_workflow/data/gch38.fa
* Entering FMI_search
* Index file found. Loading index from /scicore/home/cichon/GROUP/test_workflow/data/gch38.fa.bwt.2bit.64
* Reference seq len for bi-index = 6544178411
* sentinel-index: 2782712944
* Count:
0,  1
1,  1914743810
2,  3272089206
3,  4629434602
4,  6544178411

* Reading other elements of the index from files /scicore/home/cichon/GROUP/test_workflow/data/gch38.fa
* Index prefix: /scicore/home/cichon/GROUP/test_workflow/data/gch38.fa
* Read 0 ALT contigs
[fread] Cannot allocate memory
[main_samview] fail to read the header from "-".

Thanks