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"Could not run fq2bam" Is the only verbose output from Parabricks 4.4.0-1 and 4.3.2-1 on tutorial data - Parabricks - NVIDIA Developer Forums
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My computational environment consists of 16vCPUs, 256GB of RAM and 1 Tesla A100 (80GB). Here is my printout from the nvidia-smi: Thu Nov 28 10:00:04 2024 +---------------------------------------------------------------------------------------+ | NVIDIA-SMI 535.183.01 Driver Version: 535.183.01 CUDA Version: 12.2 | |-..." /> <meta name="twitter:description" content="Hello There I have encountered and issue that disallowes me to use parabricks, as it simply does not work, when used as presented in the fq2bam tutorial. My computational environment consists of 16vCPUs, 256GB of RAM and 1 Tesla A100 (80GB). Here is my printout from the nvidia-smi: Thu Nov 28 10:00:04 2024 +---------------------------------------------------------------------------------------+ | NVIDIA-SMI 535.183.01 Driver Version: 535.183.01 CUDA Version: 12.2 | |-..." /> <meta property="og:article:section" content="Healthcare & Life Sciences" /> <meta property="og:article:section:color" content="76B900" /> <meta property="og:article:section" content="Parabricks" /> <meta property="og:article:section:color" content="76B900" /> <meta property="og:article:tag" content="ai" /> <meta property="og:article:tag" content="demos-and-tutorials" /> <meta property="og:article:tag" content="fq2bam" /> <meta property="article:published_time" content="2024-11-28T10:03:12+00:00" /> <meta property="og:ignore_canonical" content="true" /> <script type="application/ld+json">{"@context":"http://schema.org","@type":"QAPage","name":"\"Could not run fq2bam\" Is the only verbose output from Parabricks 4.4.0-1 and 4.3.2-1 on tutorial 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href="/t/could-not-run-fq2bam-is-the-only-verbose-output-from-parabricks-4-4-0-1-and-4-3-2-1-on-tutorial-data/315052">"Could not run fq2bam" Is the only verbose output from Parabricks 4.4.0-1 and 4.3.2-1 on tutorial data</a> </h1> <div class="topic-category" itemscope itemtype="http://schema.org/BreadcrumbList"> <span itemprop="itemListElement" itemscope itemtype="http://schema.org/ListItem"> <a href="/c/healthcare/parabricks/290" class="badge-wrapper bullet" itemprop="item"> <span class='badge-category-bg' style='background-color: #76B900'></span> <span class='badge-category clear-badge'> <span class='category-name' itemprop='name'>Healthcare & Life Sciences</span> </span> </a> <meta itemprop="position" content="1" /> </span> <span itemprop="itemListElement" itemscope itemtype="http://schema.org/ListItem"> <a href="/c/healthcare/parabricks/290" class="badge-wrapper bullet" itemprop="item"> <span class='badge-category-bg' style='background-color: #76B900'></span> <span 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content='2024-11-28T10:03:12Z'> <meta itemprop='articleSection' content='Parabricks'> <meta itemprop='keywords' content='ai, demos-and-tutorials, fq2bam'> <div itemprop='publisher' itemscope itemtype="http://schema.org/Organization"> <meta itemprop='name' content='NVIDIA'> <div itemprop='logo' itemscope itemtype="http://schema.org/ImageObject"> <meta itemprop='url' content='https://global.discourse-cdn.com/nvidia/original/3X/a/1/a1ef6e0c1fbd3fad5bf82538b78dfaa9c5fa1a61.png'> </div> </div> <div id='post_1' class='topic-body crawler-post'> <div class='crawler-post-meta'> <span class="creator" itemprop="author" itemscope itemtype="http://schema.org/Person"> <a itemprop="url" href='https://forums.developer.nvidia.com/u/michal66'><span itemprop='name'>michal66</span></a> </span> <link itemprop="mainEntityOfPage" href="https://forums.developer.nvidia.com/t/could-not-run-fq2bam-is-the-only-verbose-output-from-parabricks-4-4-0-1-and-4-3-2-1-on-tutorial-data/315052"> <span class="crawler-post-infos"> <time datetime='2024-11-28T10:03:12Z' class='post-time'> November 28, 2024, 10:03am </time> <meta itemprop='dateModified' content='2024-11-28T10:03:12Z'> <span itemprop='position'>1</span> </span> </div> <div class='post' itemprop='text'> <h1><a name="p-1528585-hello-there-1" class="anchor" href="#p-1528585-hello-there-1"></a>Hello There</h1> <p>I have encountered and issue that disallowes me to use parabricks, as it simply does not work, when used as presented in the fq2bam tutorial.</p> <p>My computational environment consists of 16vCPUs, 256GB of RAM and 1 Tesla A100 (80GB).</p> <p>Here is my printout from the nvidia-smi:</p> <pre><code class="lang-auto">Thu Nov 28 10:00:04 2024 +---------------------------------------------------------------------------------------+ | NVIDIA-SMI 535.183.01 Driver Version: 535.183.01 CUDA Version: 12.2 | |-----------------------------------------+----------------------+----------------------+ | GPU Name Persistence-M | Bus-Id Disp.A | Volatile Uncorr. ECC | | Fan Temp Perf Pwr:Usage/Cap | Memory-Usage | GPU-Util Compute M. | | | | MIG M. | |=========================================+======================+======================| | 0 NVIDIA A100-SXM4-80GB Off | 00000000:00:10.0 Off | 0 | | N/A 23C P0 49W / 500W | 0MiB / 81920MiB | 0% Default | | | | Disabled | +-----------------------------------------+----------------------+----------------------+ +---------------------------------------------------------------------------------------+ | Processes: | | GPU GI CI PID Type Process name GPU Memory | | ID ID Usage | |=======================================================================================| | No running processes found | +---------------------------------------------------------------------------------------+ </code></pre> <p>My command, for running the fq2bam does not differ greatly from the original one from the tutorial (which also does not work properly) that i have tried, returns the least informative log i have had ever see. Literally no information can be inferred from that printout.</p> <pre><code class="lang-auto">Please visit https://docs.nvidia.com/clara/#parabricks for detailed documentation /usr/local/parabricks/run_pb.py fq2bam --num-gpus 1 --x3 --verbose --memory-limit 60 --bwa-options=-K 19 --ref /workdir/parabricks_sample/Ref/Homo_sapiens_assembly38.fasta --in-fq /workdir/parabricks_sample/Data/sample_1.fq.gz /workdir/parabricks_sample/Data/sample_2.fq.gz --out-bam /outputdir/fq2bam_output.bam --tmp-dir //1U548PMS [Parabricks Options Mesg]: Checking argument compatibility [Parabricks Options Mesg]: Automatically generating ID prefix [Parabricks Options Mesg]: Read group created for /workdir/parabricks_sample/Data/sample_1.fq.gz and /workdir/parabricks_sample/Data/sample_2.fq.gz [Parabricks Options Mesg]: @RG\tID:HK3TJBCX2.1\tLB:lib1\tPL:bar\tSM:sample\tPU:HK3TJBCX2.1 /usr/local/parabricks/binaries/bin/pbbwa /workdir/parabricks_sample/Ref/Homo_sapiens_assembly38.fasta --mode pair-ended-gpu /workdir/parabricks_sample/Data/sample_1.fq.gz /workdir/parabricks_sample/Data/sample_2.fq.gz -R @RG\tID:HK3TJBCX2.1\tLB:lib1\tPL:bar\tSM:sample\tPU:HK3TJBCX2.1 --nGPUs 1 --nstreams 4 --cpu-thread-pool 16 -K 19 -F 0 --min-read-size 1 --max-read-size 480 --markdups --write-bin --verbose For technical support visit https://docs.nvidia.com/clara/index.html#parabricks Exiting... Could not run fq2bam Exiting pbrun ... </code></pre> <p>And the command that I have used is here:</p> <pre><code class="lang-auto">docker run --gpus all --rm --volume $(pwd):/workdir --volume $(pwd):/outputdir nvcr.io/nvidia/clara/clara-parabricks:4.4.0-1 pbrun fq2bam --num-gpus 1 --x3 --verbose --memory-limit 60 --bwa-options="-K 19" --ref /workdir/parabricks_sample/Ref/Homo_sapiens_assembly38.fasta --in-fq /workdir/parabricks_sample/Data/sample_1.fq.gz /workdir/parabricks_sample/Data/sample_2.fq.gz --out-bam /outputdir/fq2bam_output.bam </code></pre> <p>What would be the solution for that issue?</p> </div> <div itemprop="interactionStatistic" itemscope itemtype="http://schema.org/InteractionCounter"> <meta itemprop="interactionType" content="http://schema.org/LikeAction"/> <meta itemprop="userInteractionCount" content="0" /> <span class='post-likes'></span> </div> </div> </div> <div id="related-topics" class="more-topics__list " role="complementary" 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