parabricks-nextflow execution Error reports as " bash: aws: command not found"

[sandanar]

HI PB Team,

I try to run parabricks-nextflow with aws-batch GPU accelerator and am stuck with "bash: aws: command not found" . Appreciate if you could share any pointers to fix this. Thanks you

My process aws2.nf.conf is below. Batch queue (pb-jq2) has batch compute environment with g4dn.12xlarge ['nvidia-tesla-t4']

withLabel: cloudg5 {
      executor = 'awsbatch'
      queue = 'pb-jq2'
      container = 'nvcr.io/nvidia/clara/clara-parabricks:4.1.1-1'
      accelerator = ["type": "GPU", "request": "4"]      
      disk = "1000 GB"
  }

Execution and error log is as follows:

parabricks-nextflow % nextflow run \         
    -c config/aws2.nf.conf \
    -params-file test_fq2bam2_sg.json \
    -work-dir 's3://apj-xdrefgty/nvidia/temp' \
    nextflow/fq2bam.nf
N E X T F L O W  ~  version 23.04.1
Launching `nextflow/fq2bam.nf` [sleepy_ride] DSL2 - revision: 8011563c05
executor >  awsbatch (1)
[bc/feaed3] process > ClaraParabricks_fq2bam:fq2bam [  0%] 0 of 1
executor >  awsbatch (1)
[bc/feaed3] process > ClaraParabricks_fq2bam:fq2bam [100%] 1 of 1, failed: 1 ✘
ERROR ~ Error executing process > 'ClaraParabricks_fq2bam:fq2bam'

Caused by:
  Essential container in task exited

Command executed:

  mkdir -p fq2bam &&     time /usr/local/parabricks/pbrun fq2bam     --tmp-dir fq2bam     --in-fq HG002-NA24385-pFDA_S2_L002_R1_001-5x.fastq.gz HG002-NA24385-pFDA_S2_L002_R2_001-5x.fastq.gz     --ref Homo_sapiens_assembly38.fasta     --out-bam HG002-NA24385-pFDA_S2_L002_R1_001-5x.fastq.pb.bam     --knownSites Homo_sapiens_assembly38.known_indels.vcf.gz     --out-recal-file HG002-NA24385-pFDA_S2_L002_R1_001-5x.fastq.pb.BQSR-REPORT.txt

Command exit status:
  127

Command output:
  (empty)

Command error:
  bash: aws: command not found
  bash: line 1: aws: command not found

Work dir:
  s3://apj-xdrefgty/nvidia/temp/bc/feaed38707003480c1aaca1773cbd9

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- Check '.nextflow.log' file for details