Trying to create a .bam file without the need for a .sam file

Question

I'm trying to use the code specified in this link to create a .bam file without the need for a .sam file.
Here is the code I'm using:
bwa mem -R "@RGtID:$SAMPLEtPL:illuminatSM:$SAMPLE" 
    $REF_PATH/hg38.fasta 
    mapping/R1.fastq.gz 
    mapping/R2.fastq.gz | 
    samtools sort - | 
    tee mapping/$SAMPLE.bam | 
    samtools index - mapping/$SAMPLE.bam.bai 
    2>> log

and I get the following error:
[M::bwa_idx_load_from_disk] read 0 ALT contigs
`[E::main_mem] fail to open file ` '.

The ref path and file locations work when creating and converting a .sam to a .bam file.
Any ideas?

Bastian Schiffthaler · Accepted Answer

This is an error from bwa saying that it can't find your input files:
Here's a checklist:

Check that you have no whitespace after your  newline breaks. I.e.  is the very last character
Check that you have no whitespace in any path names
Quote your variables: $REF_PATH -> "$REF_PATH"
Use set -x at the top of your bash script to debug.
In general, read this

swbarnes2 · Answer

Why make this so complicated with the tee command?
I don't think you even can index an unsorted bam, so you have to wait until sorting is done before you index.  Indexing is really short compared to mapping and sorting, you aren't saving much by trying to do both at once.

Trying to create a .bam file without the need for a .sam file

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