text: user2141: I am trying to implement Nvidia-parabrick fq2bam pipeline to process my WES dataset. The reason for opting this pipeline is the huge number of samples (1004) which take many months to process for somatic mutation identification. THe GPU accelerated pipeline will be more helpful to get somatic mutations in a quick manner. After pulling parabrick docker image from here, the following command works fine and return the options :
  
  docker run -it nvcr.io/hpc/parabricks:v2.5.0 -h
  
  But whenever I give the following command to run fq2bam pipeline, I am getting an error of No such file or directory:
  
  docker run -it nvcr.io/hpc/parabricks:v2.5.0 fq2bam --ref ucsc.hg19.fasta --in-fq sample_1.fastq.gz sample_2.fastq.gz --knownSites 1000G_phase1.indels.hg19.sites.vcf.gz --out-bam sample_dups_gpu.bam out-recal-file sample_recal_gpu.txt --tmp-dir /tmp
  
  The error is as follows:
  Traceback (most recent call last):
  File "/parabricks/run_pipeline.py", line 7, in <module>
  sys.exit(PB.pb_main())
  File "PB.pyx", line 846, in PB.pb_main
  File "/parabricks/pbargs.py", line 1287, in getArgs
  return PBRun(sys.argv)
  File "/parabricks/pbargs.py", line 392, in __init__
  self.runArgs = getattr(self, args.command)(argList)
  File "/parabricks/pbargs.py", line 447, in fq2bam
  self.addToParser(bsmb_parser_sysgroup, sysOptionGenerator().allOptions)
  File "/parabricks/pbargs.py", line 50, in __init__
  PBOption(category="sysOption", name="--num-gpus", default=GetNumGPUs(), typeName=int, helpStr="Number of GPUs to use for a run")
  File "/parabricks/pbutils.py", line 48, in GetNumGPUs
  output = subprocess.check_output(["nvidia-smi", "-L"], universal_newlines=True)
  File "/usr/lib/python2.7/subprocess.py", line 567, in check_output
  process = Popen(stdout=PIPE, *popenargs, **kwargs)
  File "/usr/lib/python2.7/subprocess.py", line 711, in __init__
  errread, errwrite)
  File "/usr/lib/python2.7/subprocess.py", line 1343, in _execute_child
  raise child_exception
  OSError: [Errno 2] No such file or directory
  
  As I am using the docker image as it is,it is not clear to me which file is missing. Kindly suggest. Thanks.
  
  user2141: My query was answered by NVIDIA Parabrick developer team. The installation instruction are available at https://forums.developer.nvidia.com/uploads/short-url/t5uXsZgdMXx0G2wDcYamFl9sO2x.pdf.
  
original_text: 2141: <p>I am trying to implement Nvidia-parabrick fq2bam pipeline to process my WES dataset. The reason for opting this pipeline is the huge number of samples (1004) which take many months to process for somatic mutation identification. THe GPU accelerated pipeline will be more helpful to get somatic mutations in a quick manner. After pulling parabrick docker image from <a href="https://ngc.nvidia.com/catalog/containers/hpc:parabricks" rel="nofollow noreferrer">here</a>, the following command works fine and return the options :</p>
  <blockquote>
  <p>docker run -it nvcr.io/hpc/parabricks:v2.5.0 -h</p>
  </blockquote>
  <p>But whenever I give the following command to run fq2bam pipeline, I am getting an error of <code>No such file or directory</code>:</p>
  <blockquote>
  <p>docker run -it nvcr.io/hpc/parabricks:v2.5.0 fq2bam --ref ucsc.hg19.fasta --in-fq sample_1.fastq.gz sample_2.fastq.gz --knownSites 1000G_phase1.indels.hg19.sites.vcf.gz --out-bam sample_dups_gpu.bam out-recal-file sample_recal_gpu.txt --tmp-dir /tmp</p>
  </blockquote>
  <p>The error is as follows:</p>
  <pre><code>Traceback (most recent call last):
  File &quot;/parabricks/run_pipeline.py&quot;, line 7, in &lt;module&gt;
  sys.exit(PB.pb_main())
  File &quot;PB.pyx&quot;, line 846, in PB.pb_main
  File &quot;/parabricks/pbargs.py&quot;, line 1287, in getArgs
  return PBRun(sys.argv)
  File &quot;/parabricks/pbargs.py&quot;, line 392, in __init__
  self.runArgs = getattr(self, args.command)(argList)
  File &quot;/parabricks/pbargs.py&quot;, line 447, in fq2bam
  self.addToParser(bsmb_parser_sysgroup, sysOptionGenerator().allOptions)
  File &quot;/parabricks/pbargs.py&quot;, line 50, in __init__
  PBOption(category=&quot;sysOption&quot;, name=&quot;--num-gpus&quot;, default=GetNumGPUs(), typeName=int, helpStr=&quot;Number of GPUs to use for a run&quot;)
  File &quot;/parabricks/pbutils.py&quot;, line 48, in GetNumGPUs
  output = subprocess.check_output([&quot;nvidia-smi&quot;, &quot;-L&quot;], universal_newlines=True)
  File &quot;/usr/lib/python2.7/subprocess.py&quot;, line 567, in check_output
  process = Popen(stdout=PIPE, *popenargs, **kwargs)
  File &quot;/usr/lib/python2.7/subprocess.py&quot;, line 711, in __init__
  errread, errwrite)
  File &quot;/usr/lib/python2.7/subprocess.py&quot;, line 1343, in _execute_child
  raise child_exception
  OSError: [Errno 2] No such file or directory
  </code></pre>
  <p>As I am using the docker image as it is,it is not clear to me which file is missing. Kindly suggest. Thanks.</p>
   2141: <p>My query was answered by NVIDIA Parabrick developer team. The installation instruction are available at <a href="https://forums.developer.nvidia.com/uploads/short-url/t5uXsZgdMXx0G2wDcYamFl9sO2x.pdf" rel="nofollow noreferrer">https://forums.developer.nvidia.com/uploads/short-url/t5uXsZgdMXx0G2wDcYamFl9sO2x.pdf</a>.</p>
  