<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>

CC BY-SA 4.0
2021-01-06T13:40:03.117Z
2021-01-06T13:40:03.117Z
Lot_to_learn
<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>

CC BY-SA 4.0
2020-12-28T12:35:57.240Z
Just a tip - if you edit your title to make it more informative (e.g. ``Nvidia Parabrick error - No such file or directory``) it helps people answer the questoin and also helps other people who have the same error.
user438383
CC BY-SA 4.0
2020-12-30T05:47:57.733Z
Thanks. I have approved the edit in question title to make it more informative.
Lot_to_learn
<sam><genomics><fastq>
Nvidia Parabrick fq2bam pipeline error - No such file or directory
# Nvidia Parabrick fq2bam pipeline error - No such file or directory

(Asked by: username_0 on 2020-12-28)

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 
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.

**Tags:** sam, genomics, fastq
> **Comments:**
> **username_1**: Just a tip - if you edit your title to make it more informative (e.g. ``Nvidia Parabrick error - No such file or directory``) it helps people answer the questoin and also helps other people who have the same error.  
> **username_0**: Thanks. I have approved the edit in question title to make it more informative.  

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## 1 answers

### Answer by username_0 on 2021-01-06. Score: 1 | Accepted answer

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>.


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