BWA mem error

Question

[gingergeiger22]

Hi, I am trying to run BWA using the following command:

module load bwa/0.7.15

time bwa mem -aCMP -t 12 -R '@RG\tID:MiSeq\tSM:VA-002\tPL:illumina\tLB:XT40 PU:Batch22' referencebasename R1_001.fastq.gz R2_001.fastq.gz > VA-002-aligned_reads.sam    

Error is:
[E::bwa_idx_load_from_disk] fail to locate the index files
real    0m0.005s
user    0m0.001s
sys     0m0.001s
/var/spool/torque/mom_priv/jobs/2184674.pbs.scm.SC: line 12: R2_001.fastq.gz: command not found

So it seems to be unable to read which of the files are my indexes and which are the read pairs? I have already ran bwa index successfully and the samtools faidx on the reference.

Thanks! Ginger

[GenoMax]

Since you are trying to use a redirect (and also have single quotes) in your command line see if this works: time "bwa mem -aCMP -t 12 -R '@RG\tID:MiSeq\tSM:VA-002\tPL:illumina\tLB:XT40 PU:Batch22' referencebasename R1_001.fastq.gz R2_001.fastq.gz > VA-002-aligned_reads.sam"