# Healthcare & Life Sciences **URL:** https://forums.developer.nvidia.com/c/healthcare/149.md?page=1 [Latest](https://forums.developer.nvidia.com/latest.md) · [Categories](https://forums.developer.nvidia.com/categories.md) · [Tags](https://forums.developer.nvidia.com/tags.md) **Page:** 2 --- ## [DiffDock and Alphafold2 API error: Internal Server Error, Inference error](https://forums.developer.nvidia.com/t/diffdock-and-alphafold2-api-error-internal-server-error-inference-error/356563)
**Author:** [@meenal\_gupta2](https://forums.developer.nvidia.com/u/meenal_gupta2)\ **Replies:** 1\ **Last updated:** [March 23, 2026, 5:41am UTC](https://forums.developer.nvidia.com/t/diffdock-and-alphafold2-api-error-internal-server-error-inference-error/356563 "2026-03-23T05:41:34Z")
Hello, I’m facing an issue with the DiffDock and AlphaFold2 NIM endpoints. DiffDock was working fine when I checked on Friday, but it’s failing now. I’m seeing the same error for the AlphaFold2 endpoint as well. I’ve ad… --- ## [Sorting clarification for markdup](https://forums.developer.nvidia.com/t/sorting-clarification-for-markdup/344171)
**Author:** [@sschuste](https://forums.developer.nvidia.com/u/sschuste)\ **Replies:** 5\ **Last updated:** [March 18, 2026, 11:32pm UTC](https://forums.developer.nvidia.com/t/sorting-clarification-for-markdup/344171 "2026-03-18T23:32:43Z")
Does Parabricks markdup assume/require the input bam to be coordinate or queryname sorted? The documentation is contradictory- it first says it supports both ways, with coordinate being the default and queryname an opti… --- ## [GenotypeGVCF in Parabricks 4.3.2 not using GPUs and ending with error](https://forums.developer.nvidia.com/t/genotypegvcf-in-parabricks-4-3-2-not-using-gpus-and-ending-with-error/363087)
**Author:** [@nacif.camila](https://forums.developer.nvidia.com/u/nacif.camila)\ **Replies:** 4\ **Last updated:** [March 17, 2026, 1:42pm UTC](https://forums.developer.nvidia.com/t/genotypegvcf-in-parabricks-4-3-2-not-using-gpus-and-ending-with-error/363087 "2026-03-17T13:42:22Z")
Hi everyone, I am trying to run GenotypeGVCF with Parabricks 4.3.2. My dataset contains 60 samples and a 3 Gb genome. I am running the job with: 2 GPUs 250 GB RAM 48 CPUs However, when I run it, it seems th… --- ## [Fq2bam stalls in single-end recovery mode](https://forums.developer.nvidia.com/t/fq2bam-stalls-in-single-end-recovery-mode/361533)
**Author:** [@jahemker](https://forums.developer.nvidia.com/u/jahemker)\ **Replies:** 3\ **Last updated:** [March 9, 2026, 3:51pm UTC](https://forums.developer.nvidia.com/t/fq2bam-stalls-in-single-end-recovery-mode/361533 "2026-03-09T15:51:38Z")
I am using parabricks fq2bam to align a ~100 samples to a reference genome. This command is integrated into a snakemake pipeline that is run on a SLURM HPCC. This has worked well for all but a few samples, which consiste… --- ## [Why was it that I was able to successfully run fq2bam but it didn't work properly?](https://forums.developer.nvidia.com/t/why-was-it-that-i-was-able-to-successfully-run-fq2bam-but-it-didnt-work-properly/362809)
**Author:** [@daxiaotouyu](https://forums.developer.nvidia.com/u/daxiaotouyu)\ **Replies:** 0\ **Last updated:** [March 9, 2026, 8:23am UTC](https://forums.developer.nvidia.com/t/why-was-it-that-i-was-able-to-successfully-run-fq2bam-but-it-didnt-work-properly/362809 "2026-03-09T08:23:21Z")
--- ## [Options for fq2bam/markdup to only handle optical duplicates and support multi-lane samples](https://forums.developer.nvidia.com/t/options-for-fq2bam-markdup-to-only-handle-optical-duplicates-and-support-multi-lane-samples/360166)
**Author:** [@PaulMatterBioDev](https://forums.developer.nvidia.com/u/PaulMatterBioDev)\ **Replies:** 1\ **Last updated:** [February 20, 2026, 8:19pm UTC](https://forums.developer.nvidia.com/t/options-for-fq2bam-markdup-to-only-handle-optical-duplicates-and-support-multi-lane-samples/360166 "2026-02-20T20:19:25Z")
I would love to see parabricks implementations of the following features currently present in GATK4’s MarkDuplicates The ability to direct markdups to only mark optical duplicates – I have non-PCR libraries in which an… --- ## [Deepsomatic Invalid tumor sample name input](https://forums.developer.nvidia.com/t/deepsomatic-invalid-tumor-sample-name-input/360529)
**Author:** [@irem.yucel](https://forums.developer.nvidia.com/u/irem.yucel)\ **Replies:** 1\ **Last updated:** [February 17, 2026, 11:08pm UTC](https://forums.developer.nvidia.com/t/deepsomatic-invalid-tumor-sample-name-input/360529 "2026-02-17T23:08:23Z")
Hey all, I am trying to run Parabricks Deepsomatic with the full command below: pbrun deepsomatic \\ –-mode=ont \\ –-ref=%(profile\_genome\_fa)s \\ --in-normal-bam=%(normal\_bam)s \\ -–in-tumor-bam=%(tumor\_bam)s \\ --out-varia… --- ## [Minimap signal error](https://forums.developer.nvidia.com/t/minimap-signal-error/360531)
**Author:** [@irem.yucel](https://forums.developer.nvidia.com/u/irem.yucel)\ **Replies:** 0\ **Last updated:** [February 13, 2026, 12:43pm UTC](https://forums.developer.nvidia.com/t/minimap-signal-error/360531 "2026-02-13T12:43:11Z")
Hey all, I am trying to run minimap2 with parabricks, with the full command below: pbrun minimap2 \\ --ref "%(profile\_genome\_fa)s" \\ --in-bam "%(input)s" \\ --out-bam "%(output\_dir)s/%(sample\_name)s.bam" \\ --pres… --- ## [Setting PAR position in DeepVariant](https://forums.developer.nvidia.com/t/setting-par-position-in-deepvariant/360009)
**Author:** [@hollo.gergo00](https://forums.developer.nvidia.com/u/hollo.gergo00)\ **Replies:** 0\ **Last updated:** [February 8, 2026, 6:23pm UTC](https://forums.developer.nvidia.com/t/setting-par-position-in-deepvariant/360009 "2026-02-08T18:23:34Z")
Dear Everyone! We have recently switched to NVIDIA Parabricks for our germline variant calling pipeline, however we have trouble with variant calling on the Y chromosome. Unfortunately I can only see the –haploid-conti… --- ## [Testing with WGS](https://forums.developer.nvidia.com/t/testing-with-wgs/359233)
**Author:** [@itagipushpa](https://forums.developer.nvidia.com/u/itagipushpa)\ **Replies:** 0\ **Last updated:** [January 31, 2026, 9:25pm UTC](https://forums.developer.nvidia.com/t/testing-with-wgs/359233 "2026-01-31T21:25:52Z")
Hello, I have used Parabricks to align WGS samples in my research and found it to be very fast and efficient. I am interested in applying it more broadly. I was wondering whether Parabricks has been extensively tested f… --- ## [Minimap2 presets](https://forums.developer.nvidia.com/t/minimap2-presets/358355)
**Author:** [@a.kurdadze](https://forums.developer.nvidia.com/u/a.kurdadze)\ **Replies:** 0\ **Last updated:** [January 22, 2026, 5:20pm UTC](https://forums.developer.nvidia.com/t/minimap2-presets/358355 "2026-01-22T17:20:54Z")
Can we add the asm5, asm10, and asm20 presets to pbrun minimap2? Right now it seems limited to read mapping (map-hifi, map-ont..), but having the assembly presets would be huge for moving our assembly QC workflows to G… --- ## [Memory issues while running Marking Duplicates and BQSR](https://forums.developer.nvidia.com/t/memory-issues-while-running-marking-duplicates-and-bqsr/320758)
**Author:** [@mihaela.thiele](https://forums.developer.nvidia.com/u/mihaela.thiele)\ **Replies:** 3\ **Last updated:** [January 16, 2026, 4:16am UTC](https://forums.developer.nvidia.com/t/memory-issues-while-running-marking-duplicates-and-bqsr/320758 "2026-01-16T04:16:16Z")
Hello, I started recentyl using Parabricks and run into an issue related to the marking duplicates and BQSR step in the fq2bam method. I hope to get some hints on how to fix this. I get the following error message: \[P… --- ## [Genotype-only mode with HaplotypeCaller](https://forums.developer.nvidia.com/t/genotype-only-mode-with-haplotypecaller/357057)
**Author:** [@lorenzovb141](https://forums.developer.nvidia.com/u/lorenzovb141)\ **Replies:** 0\ **Last updated:** [January 9, 2026, 2:03am UTC](https://forums.developer.nvidia.com/t/genotype-only-mode-with-haplotypecaller/357057 "2026-01-09T02:03:29Z")
Hello! I am trying to run Parabricks HaplotypeCaller in genotype-only mode. I.e., i have a set of sites from two parents sequenced at 60x coverage, and I would like to genotype offspring sequenced at 10x from those pare… --- ## [Deepvariant fails with cram file, OK with bam](https://forums.developer.nvidia.com/t/deepvariant-fails-with-cram-file-ok-with-bam/353321)
**Author:** [@shaze](https://forums.developer.nvidia.com/u/shaze)\ **Replies:** 7\ **Last updated:** [January 5, 2026, 5:02pm UTC](https://forums.developer.nvidia.com/t/deepvariant-fails-with-cram-file-ok-with-bam/353321 "2026-01-05T17:02:53Z")
Dear all I would be grateful for any help with this problem that’s taken many hours My call to pbrun deepvariant on a cram file fails with this error PB Info 2025-Dec-02 18:33:43\] Starting DeepVariant\[PB Info 2025-Dec… --- ## [Do researchers or students need a license to use Clara Parabricks?](https://forums.developer.nvidia.com/t/do-researchers-or-students-need-a-license-to-use-clara-parabricks/356023)
**Author:** [@1029304573](https://forums.developer.nvidia.com/u/1029304573)\ **Replies:** 0\ **Last updated:** [December 29, 2025, 11:44am UTC](https://forums.developer.nvidia.com/t/do-researchers-or-students-need-a-license-to-use-clara-parabricks/356023 "2025-12-29T11:44:34Z")
Do researchers or students need a license to use Clara Parabricks? --- ## [NVIDIA Parabricks fq2bam performance](https://forums.developer.nvidia.com/t/nvidia-parabricks-fq2bam-performance/352772)
**Author:** [@alex990713](https://forums.developer.nvidia.com/u/alex990713)\ **Replies:** 1\ **Last updated:** [December 17, 2025, 5:53pm UTC](https://forums.developer.nvidia.com/t/nvidia-parabricks-fq2bam-performance/352772 "2025-12-17T17:53:38Z")
I am currently evaluating the GPU version of Parabricks and would like to clarify the performance and compatibility details related to GPU specifications. According to the documentation, the minimum GPU memory requireme… --- ## [Alphafold multimer issue](https://forums.developer.nvidia.com/t/alphafold-multimer-issue/353354)
**Author:** [@vishwambhar.bhandare](https://forums.developer.nvidia.com/u/vishwambhar.bhandare)\ **Replies:** 0\ **Last updated:** [December 3, 2025, 1:50am UTC](https://forums.developer.nvidia.com/t/alphafold-multimer-issue/353354 "2025-12-03T01:50:59Z")
Alphafold multimer performance issue Earlier structure generation time was 7 min / structure on H100 machine Now it takes ~ 30 mins on same H100 machine from different vendor. Our DevOps team tried troubleshooting the… --- ## [MONAI Discussions can now be found on GitHub](https://forums.developer.nvidia.com/t/monai-discussions-can-now-be-found-on-github/353326)
**Author:** [@TomNVIDIA](https://forums.developer.nvidia.com/u/TomNVIDIA)\ **Replies:** 0\ **Last updated:** [December 2, 2025, 5:25pm UTC](https://forums.developer.nvidia.com/t/monai-discussions-can-now-be-found-on-github/353326 "2025-12-02T17:25:32Z")
--- ## [Are you considering adding H-C data comparison to the framework?](https://forums.developer.nvidia.com/t/are-you-considering-adding-h-c-data-comparison-to-the-framework/351706)
**Author:** [@1004803499](https://forums.developer.nvidia.com/u/1004803499)\ **Replies:** 3\ **Last updated:** [December 2, 2025, 6:31am UTC](https://forums.developer.nvidia.com/t/are-you-considering-adding-h-c-data-comparison-to-the-framework/351706 "2025-12-02T06:31:39Z")
Dear developer, Thank you very much for developing such an excellent tool. It has been extremely useful for our resequencing data analyses. I would like to ask a question regarding its performance with Hi-C data. When … --- ## [Open fold issue](https://forums.developer.nvidia.com/t/open-fold-issue/353253)
**Author:** [@vishwambhar.bhandare](https://forums.developer.nvidia.com/u/vishwambhar.bhandare)\ **Replies:** 0\ **Last updated:** [December 2, 2025, 5:05am UTC](https://forums.developer.nvidia.com/t/open-fold-issue/353253 "2025-12-02T05:05:04Z")
While testing openfold for antibody light and heavy chain structure generation, we are facing an issue on Multiple sequence alignment (MSA) as input. It seems, all MSA inputs requires same length. In general, alphafold d… --- ## [Remote internship or Master Thesis collaborations](https://forums.developer.nvidia.com/t/remote-internship-or-master-thesis-collaborations/353041)
**Author:** [@claudiapascualtomas99](https://forums.developer.nvidia.com/u/claudiapascualtomas99)\ **Replies:** 0\ **Last updated:** [November 30, 2025, 5:00pm UTC](https://forums.developer.nvidia.com/t/remote-internship-or-master-thesis-collaborations/353041 "2025-11-30T17:00:34Z")
I’m a MSc Bioinformatics student interested in BioNeMo research and would like to know whether NVIDIA collaborates with students through remote internships or thesis projects. Who would be the right person or team to con… --- ## [IMX334 CSI Camera interface with Jetson orin NX](https://forums.developer.nvidia.com/t/imx334-csi-camera-interface-with-jetson-orin-nx/348951)
**Author:** [@rnd25](https://forums.developer.nvidia.com/u/rnd25)\ **Replies:** 1\ **Last updated:** [November 10, 2025, 4:21pm UTC](https://forums.developer.nvidia.com/t/imx334-csi-camera-interface-with-jetson-orin-nx/348951 "2025-11-10T16:21:59Z")
Hello, I am new to Jetson Orion NX. Below is my setup details, Baord : Jetson Orion NX SDK: Jetpack 6.2 Camera : IMX334 The first trial with Arducam IMX477 was successful at 4K, 30fps. The second trail with sensor … --- ## [DeepVariant is deepsomatic?](https://forums.developer.nvidia.com/t/deepvariant-is-deepsomatic/349757)
**Author:** [@sam.talbot](https://forums.developer.nvidia.com/u/sam.talbot)\ **Replies:** 1\ **Last updated:** [November 3, 2025, 10:48pm UTC](https://forums.developer.nvidia.com/t/deepvariant-is-deepsomatic/349757 "2025-11-03T22:48:27Z")
Hello, I am a bit concerned about the usage of deepvariant as it exists in 4.6.0. Whether I call pangenome\_aware\_deepvariant or deepvariant both seem to actually call deepsomatic. Deepsomatic has a different training … --- ## [Human-GPU Convergence in Health & Oncology — BPM RED Academy HumAI PoV on Llama 3.3 70B Instruct](https://forums.developer.nvidia.com/t/human-gpu-convergence-in-health-oncology-bpm-red-academy-humai-pov-on-llama-3-3-70b-instruct/349579)
**Author:** [@bpm\_red\_academy](https://forums.developer.nvidia.com/u/bpm_red_academy)\ **Replies:** 0\ **Last updated:** [October 30, 2025, 11:41am UTC](https://forums.developer.nvidia.com/t/human-gpu-convergence-in-health-oncology-bpm-red-academy-humai-pov-on-llama-3-3-70b-instruct/349579 "2025-10-30T11:41:53Z")
We are thrilled to share our latest work at BPM RED Academy: a full proof-of-value suite for Health and Oncology built on Llama 3.3 70B Instruct and deployed within the Hyperstack × NVIDIA ecosystem. Key Highlights: L… --- ## [Since our chromosomes are too large, could you please add support for the CSI index in the next update?](https://forums.developer.nvidia.com/t/since-our-chromosomes-are-too-large-could-you-please-add-support-for-the-csi-index-in-the-next-update/349339)
**Author:** [@2432091670](https://forums.developer.nvidia.com/u/2432091670)\ **Replies:** 1\ **Last updated:** [October 29, 2025, 6:46am UTC](https://forums.developer.nvidia.com/t/since-our-chromosomes-are-too-large-could-you-please-add-support-for-the-csi-index-in-the-next-update/349339 "2025-10-29T06:46:14Z")
Since our chromosomes are too large, could you please add support for the CSI index in the next update? --- ## [Outdated vg](https://forums.developer.nvidia.com/t/outdated-vg/348654)
**Author:** [@sam.talbot](https://forums.developer.nvidia.com/u/sam.talbot)\ **Replies:** 1\ **Last updated:** [October 28, 2025, 6:18pm UTC](https://forums.developer.nvidia.com/t/outdated-vg/348654 "2025-10-28T18:18:34Z")
Hi is there a reason why parabricks uses vg version 1.59 from over a year ago? It has some serious errors that have since been addressed in many releases. For example, if the rescue attempt fails, Giraffe is supposed to … --- ## [Latest Parabricks Releases](https://forums.developer.nvidia.com/t/latest-parabricks-releases/300179)
**Author:** [@carolinew](https://forums.developer.nvidia.com/u/carolinew)\ **Replies:** 4\ **Last updated:** [October 21, 2025, 5:10pm UTC](https://forums.developer.nvidia.com/t/latest-parabricks-releases/300179 "2025-10-21T17:10:13Z")
New features, performance improvements and bug fixes by release. --- ## [Support for --quantMode TranscriptomeSAM in STAR alignment with Parabricks?](https://forums.developer.nvidia.com/t/support-for-quantmode-transcriptomesam-in-star-alignment-with-parabricks/328997)
**Author:** [@chouch7](https://forums.developer.nvidia.com/u/chouch7)\ **Replies:** 1\ **Last updated:** [October 20, 2025, 9:46pm UTC](https://forums.developer.nvidia.com/t/support-for-quantmode-transcriptomesam-in-star-alignment-with-parabricks/328997 "2025-10-20T21:46:34Z")
Hi, I’m wondering if the --quantMode TranscriptomeSAM option for STAR alignment is supported in NVIDIA Parabricks. This option is commonly used for downstream quantification tools like RSEM or Salmon. If not currently s… --- ## [Is it possible to support STARsolo features in rna\_fq2bam](https://forums.developer.nvidia.com/t/is-it-possible-to-support-starsolo-features-in-rna-fq2bam/278918)
**Author:** [@cheneypku](https://forums.developer.nvidia.com/u/cheneypku)\ **Replies:** 2\ **Last updated:** [October 20, 2025, 9:43pm UTC](https://forums.developer.nvidia.com/t/is-it-possible-to-support-starsolo-features-in-rna-fq2bam/278918 "2025-10-20T21:43:41Z")
Hi Parabricks Team, I hope you’re all doing well! I’m reaching out to discuss a potential enhancement to the rna\_fq2bam tool in the Parabricks suite that I think many users, myself included, would find super valuable. I… --- ## [Starsolo?](https://forums.developer.nvidia.com/t/starsolo/341470)
**Author:** [@nick.youngblut](https://forums.developer.nvidia.com/u/nick.youngblut)\ **Replies:** 1\ **Last updated:** [October 20, 2025, 9:40pm UTC](https://forums.developer.nvidia.com/t/starsolo/341470 "2025-10-20T21:40:47Z")
The parabricks paper states: Its GPU-accelerated workflows extend to RNAseq analysis, leveraging tools such as STAR \[25\], STARsolo, and STAR-Fusion \[26\] for rapid and scalable transcriptomic data processin However, t… [Previous page](https://forums.developer.nvidia.com/c/healthcare/149.md) [Next page](https://forums.developer.nvidia.com/c/healthcare/149.md?page=2)