I receive the error above when attempting the following code:

bwa mem -t 24 /home/devan/projects/rrg-shaferab/devan/Odocoileus_virginianus/ref_fasta/odocoileus_virginianus_New
$Path/$SP/trimmed_seq/AD014_S35_L003_R1_001.fastq.gz/AD014_S35_L003_R1_001.clean.fq.gz
$Path/$SP/trimmed_seq/AD014_S35_L003_R1_001.fastq.gz/AD014_S35_L003_R2_001.clean.fq.gz | 
samtools sort -m 5G -@24 -O bam -T /home/devan/projects/rrg-shaferab/devan/Odocoileus_virginianus/bam_files/AD014_M_0.sorted 
-o /home/devan/projects/rrg-shaferab/devan/Odocoileus_virginianus/bam_files/AD014_M_0.sorted.bam

The formatting of the files is odd as there is a folder named AD014_S35_L003_R1_001.fastq.gz. Personally I wouldn’t have done this but I am following a bioinformatics pipeline.

echo $Path returns /home/devan/projects/rrg-shaferab/devan

echo $SP returns Odocoileus_virginianus

I expected to be mapping the trimmed sequences to the reference genome by running this. I have looked through the questions others have asked and none of the solutions have worked for me. If anyone can help it would be greatly appreciated. Thanks!