NVIDIA / Parabricks / 軟體下載與安裝(v1) === ###### tags: `Parabricks-v3.1` ###### tags: `基因體`, `NVIDIA`, `Clara`, `Parabricks`, `二級分析` <br> [TOC] <br> ## 測試方法一 (向 Nvidia 請求授權下載 Parabricks) 1. ### 前往 [NVIDIA CLARA PARABRICKS 首頁](https://www.nvidia.com/zh-tw/healthcare/clara-parabricks/) - https://www.nvidia.com/zh-tw/healthcare/clara-parabricks/ - https://www.nvidia.com/en-us/healthcare/clara-parabricks/ - [FREE ONE-MONTH TRIAL](https://www.nvidia.com/en-us/docs/nvidia-parabricks-general/) 2. ### 點選 [免費試用一個月](https://www.nvidia.com/en-us/docs/nvidia-parabricks-general/) ![](https://i.imgur.com/cWzj5oy.png) - 備註 - ==每個帳戶只能發一次請求，第二次以後就不受理== - 同一個帳戶發了第二次、第三次都沒收到 - 換了新帳戶後，第一次有收到回應，第二次又沒收到 3. ### 填寫基本資料後送出 ![](https://i.imgur.com/4gjiArg.png) - 填寫 ASUS mail 都會收不到 - 填寫 gmail 可以收到 (2021/06/01 確認) 4. ### 收到 mail 通知 (gmail: 有可能跑到促銷廣告裡) - 舊版 [![](https://i.imgur.com/1U76c00.png)](https://i.imgur.com/1U76c00.png) <br> :::info :information_source: **CLARA PARABRICKS PIPELINES EVAL** <br> Thank you for requesting access to NVIDIA Clara Parabricks Pipelines. Below is your license key for your free 1-month evaluation to Parabricks Pipelines. <br> **[Install Parabricks Pipelines](http://go.nvidianews.com/HO000690MaZgvNdn6vF00YE)** <br> To help get you started with quick-start guides, please visit our **[documentation page](https://www.nvidia.com/en-us/docs/parabricks/)**. <br> If you have any questions, please reach out to us on our **[developer forums](http://go.nvidianews.com/Bv060O0NM000dnvF0gZ6a9E)**. <br> For use on DNANexus, please follow the **[instructions](http://go.nvidianews.com/P060MnEO6F0a0d0w0g2Nv90)** using the license file from the install link above. <br> Thank you, The NVIDIA Parabricks team ::: - 論壇(forum)：https://forums.developer.nvidia.com/c/healthcare/Parabricks <br> 5. ### 點選 [Install Parabricks Pipelines](http://go.nvidianews.com/HO000690MaZgvNdn6vF00YE) 6. ### 網址自動導向到 https://s3.amazonaws.com/parabricks.licenses/v311_NOV_END/parabricks.tar.gz?AWSAccessKeyId=... ![](https://i.imgur.com/hmbRynA.png) - 「請求日」超過「過期日」(程式的 bug) - 請求日：2020-10-26 - 過期日：2020-10-21 - [[Nvidia][Forum] How could I try clara parabricks?](https://forums.developer.nvidia.com/t/how-could-i-try-clara-parabricks/157689) 7. ### 結論 失敗，無法取得 Parabricks 軟體 預期的[下載檔內容](https://www.nvidia.com/en-us/docs/parabricks/local-installation/)，應該有 - installer.py: Installer to download and install the software - license.bin: License file based on your license with NVIDIA Parabricks - EULA.txt: End User License Agreement <br> <hr> <br> ## ~~測試方法二 (它是透過 container 執行，但無 license.bin，執行會被拒)~~ 1. ### 輸入關鍵字尋找 ![](https://i.imgur.com/q0zKIV7.png) 2. ### https://ngc.nvidia.com/catalog/containers/hpc:parabricks [![](https://i.imgur.com/yol0h8D.png)](https://ngc.nvidia.com/catalog/containers/hpc:parabricks) 3. ### Pull Command ```docker pull nvcr.io/hpc/parabricks:v2.5.0``` - nvcr: Nvidia Container Release - ngc: Nvidia GPU Cloud - 目前 ngc 上，並沒有 ```nvcr.io/hpc/parabricks:v3.1.1``` ``` 'docker pull nvcr.io/hpc/parabricks:v3.1.1 Error response from daemon: manifest for nvcr.io/hpc/parabricks:v3.1.1 not found: manifest unknown: manifest unknown Cannot download Parabricks docker image. Contact Parabricks-Support@nvidia.com for troubleshooting ``` 4. ### 執行簡易 docker 測試1 - 顯示用法 ```nvidia-docker run --rm nvcr.io/hpc/parabricks:v2.5.0 -h``` 或 ```docker run --rm nvcr.io/hpc/parabricks:v2.5.0 -h``` - 參考資料：[Running with nvidia-docker](https://ngc.nvidia.com/catalog/containers/hpc:picongpu) - 實際測試：==**不需要再接 pbrun 指令，否則會有錯訊息**== ``` Unrecognized command pbrun <--- 無法識別 pbrun 指令 usage: pbrun <command> [<args>] Help: pbrun -h ``` 5. ### 執行簡易 docker 測試2 - 顯示版本 ```docker run --rm nvcr.io/hpc/parabricks:v2.5.0 --version``` 或 ```docker run --rm nvcr.io/hpc/parabricks:v2.5.0 version``` 或 ```docker run --rm nvcr.io/hpc/parabricks:v2.5.0 pbrun --version``` 6. ### 台大基因案例子 ``` docker run --rm \ -v /home/diatango_lin/tj_tsai/parabricks/dataset/D15780_S13_L001/:/dataset/ \ nvcr.io/hpc/parabricks:v2.5.0 fq2bam \ --ref /dataset/human_g1k_v37_decoy.fasta \ --in-fq /dataset/D15780_S13_L001_R1.fastq.gz /dataset/D15780_S13_L001_R2.fastq.gz \ --out-bam /dataset/out.bam ``` <br> **執行結果** ``` [Parabricks Options Mesg]: Checking argument compatibility [Parabricks Options Mesg]: Automatically generating ID prefix [Parabricks Options Mesg]: Read group created for /dataset/D15780_S13_L001_R1.fastq.gz and /dataset/D15780_S13_L001_R2.fastq.gz [Parabricks Options Mesg]: @RG\tID:000000000-C54LP.1\tLB:lib1\tPL:bar\tSM:sample\tPU:000000000-C54LP.1 License file ```license.bin``` not found in installation folder or passed in as argument Please contact support@parabricks.com for any questions. Exiting... ``` - License file license.bin not found in installation folder <br> **取得 license.bin，重新執行** ```bash # 加上 -v /home/diatango_lin/tj_tsai/software/parabricks/license.bin:/opt/parabricks/license.bin docker run --rm \ -v /home/diatango_lin/tj_tsai/software/parabricks/license.bin:/opt/parabricks/license.bin \ -v /home/diatango_lin/tj_tsai/parabricks/dataset/D15780_S13_L001/:/dataset/ \ nvcr.io/hpc/parabricks:v2.5.0 fq2bam \ --ref /dataset/human_g1k_v37_decoy.fasta \ --in-fq /dataset/D15780_S13_L001_R1.fastq.gz /dataset/D15780_S13_L001_R2.fastq.gz \ --out-bam /dataset/out.bam ``` - 根據 [installer.py](https://github.com/prabindh/parabricks-changes/blob/master/installer.py) - ```--install-location``` 預設在 "/opt/" + "/parabricks" - 結果還是一樣 ```License file license.bin not found in installation folder or passed in as argument``` - 前往論壇，詢問 Nvidia， 結果 Nvidia 回應：請使用正常管道的 trial version https://forums.developer.nvidia.com/t/nvidia-parabricks-what-is-the-correct-path-of-license-bin-in-a-container/158035 - 後來使用 trial version， 透過 docker inspect 知道：```license.bin``` 是要掛在 ```/INSTALL/``` 底下 ```bash docker run --rm \ -v /opt/parabricks/:/INSTALL/ \ -v /mnt/parabricks/dataset/D15780_S13_L001/:/dataset/ \ nvcr.io/hpc/parabricks:v2.5.0 \ fq2bam \ --ref /dataset/b37/human_g1k_v37_decoy.fasta \ --in-fq /dataset/D15780_S13_L001_R1.fastq.gz /dataset/D15780_S13_L001_R2.fastq.gz \ --out-bam /dataset/out.bam ``` 執行結果： ``` [Parabricks Options Mesg]: Checking argument compatibility [Parabricks Options Mesg]: Automatically generating ID prefix [Parabricks Options Mesg]: Read group created for /dataset/D15780_S13_L001_R1.fastq.gz and /dataset/D15780_S13_L001_R2.fastq.gz [Parabricks Options Mesg]: @RG\tID:000000000-C54LP.1\tLB:lib1\tPL:bar\tSM:sample\tPU:000000000-C54LP.1 ------------------------------------------------------------------------------ || Parabricks accelerated Genomics Pipeline || || Version v2.5.0 || || GPU-BWA mem, Sorting, Marking Duplicates, BQSR || || Contact: Parabricks-Support@nvidia.com || ------------------------------------------------------------------------------ [E::bwa_idx_load_from_disk] fail to locate the index files ------------------------------------------------------------------------------ || Program: GPU-BWA mem, Sorting, Marking Duplicates, BQSR || || Version: v2.5.0 || || Start Time: Mon Nov 2 03:56:13 2020 || || End Time: Mon Nov 2 03:56:13 2020 || || Total Time: 0 seconds || ------------------------------------------------------------------------------ Please contact support@parabricks.com for any questions. Exiting... ``` 有錯誤訊息： ``` [E::bwa_idx_load_from_disk] fail to locate the index files ``` 經過追查，起因於：「沒有完整的 fasta 索引檔」 ``` D15780_S13_L001/b37.full/ ├── human_g1k_v37_decoy.dict ├── human_g1k_v37_decoy.fasta ├── human_g1k_v37_decoy.fasta.amb ├── human_g1k_v37_decoy.fasta.ann ├── human_g1k_v37_decoy.fasta.bwt ├── human_g1k_v37_decoy.fasta.fai ├── human_g1k_v37_decoy.fasta.flat ├── human_g1k_v37_decoy.fasta.gdx ├── human_g1k_v37_decoy.fasta.pac └── human_g1k_v37_decoy.fasta.sa 0 directories, 10 files ``` <br> 變更資料來源後，再執行一次： - /dataset/b37/ 變更為 /dataset/b37.full/ ```bash docker run --rm \ -v /opt/parabricks/:/INSTALL/ \ -v /mnt/parabricks/dataset/D15780_S13_L001/:/dataset/ \ nvcr.io/hpc/parabricks:v2.5.0 \ fq2bam \ --ref /dataset/b37.full/human_g1k_v37_decoy.fasta \ --in-fq /dataset/D15780_S13_L001_R1.fastq.gz /dataset/D15780_S13_L001_R2.fastq.gz \ --out-bam /dataset/out.bam ``` <br> 執行結果： ``` [Parabricks Options Mesg]: Checking argument compatibility [Parabricks Options Mesg]: Automatically generating ID prefix [Parabricks Options Mesg]: Read group created for /dataset/D15780_S13_L001_R1.fastq.gz and /dataset/D15780_S13_L001_R2.fastq.gz [Parabricks Options Mesg]: @RG\tID:000000000-C54LP.1\tLB:lib1\tPL:bar\tSM:sample\tPU:000000000-C54LP.1 ------------------------------------------------------------------------------ || Parabricks accelerated Genomics Pipeline || || Version v2.5.0 || || GPU-BWA mem, Sorting, Marking Duplicates, BQSR || || Contact: Parabricks-Support@nvidia.com || ------------------------------------------------------------------------------ [M::bwa_idx_load_from_disk] read 0 ALT contigs GPU-BWA mem ProgressMeter Reads Base Pairs Aligned GPU-BWA Mem time: 28.461105 seconds GPU-BWA Mem is finished. GPU Sorting, Marking Dups, BQSR ProgressMeter SAM Entries Completed Total GPU-BWA Mem + Sorting + MarkingDups + BQSR Generation + BAM writing Processing time: 36.641302 seconds [main] CMD: PARABRICKS mem -Z ./pbOpts.txt /dataset/b37.full/human_g1k_v37_decoy.fasta /dataset/D15780_S13_L001_R1.fastq.gz /dataset/D15780_S13_L001_R2.fastq.gz @RG\tID:000000000-C54LP.1\tLB:lib1\tPL:bar\tSM:sample\tPU:000000000-C54LP.1 [main] Real time: 50.952 sec; CPU: 265.815 sec ------------------------------------------------------------------------------ || Program: GPU-BWA mem, Sorting, Marking Duplicates, BQSR || || Version: v2.5.0 || || Start Time: Wed Nov 4 01:13:56 2020 || || End Time: Wed Nov 4 01:14:47 2020 || || Total Time: 51 seconds || ------------------------------------------------------------------------------ ``` <br> 關於 parabricks image 的差異，個人主觀認為： - nvcr.io/hpc/parabricks:v2.5.0 ，版本是 v2.5.0 (~~然後也無法正確讀取 index files~~) - parabricks/release:v3.1.1 ，版本是 v3.1.1，應該是全新改版 上述已發布在 [[Nvidia/Parabricks] What is the correct path of license.bin in a container?](https://forums.developer.nvidia.com/t/nvidia-parabricks-what-is-the-correct-path-of-license-bin-in-a-container/158035) <br> <hr> <br> ## 測試方法三 (成功) - ### [[Nvidia][Forum]](https://forums.developer.nvidia.com/c/healthcare/Parabricks/290?ncid=em-prod-75940&mkt_tok=eyJpIjoiTkRaa05UYzRZek13TnpnMSIsInQiOiJoS1RSdVFLNlIwOEI3Wk1hOFVlYnVHbnZaa1Z6emJhUERWMXpvVWJxbk1ETXNVSmZVZml6czdFbXFlcmc1XC9JVVVQV21LdU5qZXlvQVFHajBiWmxOUUVRc1lDaFpTZmNLRG1qZlJocDI5b1l6dlBjV0E5blJoV1ByY3MxUDlBZXEifQ%3D%3D) - [How could I try clara parabricks?](https://forums.developer.nvidia.com/t/how-could-i-try-clara-parabricks/157689) > Greetings, Our apologies for this mishap; it appears that there’s a new policy for the link expiration that we’ll be addressing separately - here’s an updated link pointer for you to use instead: > > wget -O parabricks.tar.gz "https://s3.amazonaws.com/parabricks.licenses/v311_NOV_END/parabricks.tar.gz?AWSAccessKeyId=AKIAJGDUNN2G2ZAH3Q3A&Signature=MzWbwsjmXWdzyACJT2JUH1XlMAs%3D&Expires=1608564579" - [Evaluation License Download Links Are Invalid](https://forums.developer.nvidia.com/t/evaluation-license-download-links-are-invalid/157233) (expired!!) > Hi, thanks for reaching out to us. Could you please try the following link, which expires at the end of Nov? "https://s3.amazonaws.com/parabricks.licenses/v311_NOV_END/parabricks.tar.gz?AWSAccessKeyId=AKIAJGDUNN2G2ZAH3Q3A&Expires=1603296915&Signature=7LXvM92YJvFxRuXRA5WSPNnxLPU%3D" Thank you! - ### ==詳細的執行結果，請參考== [[Hackmd] NVIDIA / Parabricks / docker inspect …](/dicZf7wIT_6P_cqASd2EDQ) <br> <hr> <br> ## 測試方法一 (接續)(新版 2021/06/02) [![](https://i.imgur.com/lsg7bK0.png)](https://i.imgur.com/lsg7bK0.png) <br> [![](https://i.imgur.com/GKQTVxZ.png)](https://i.imgur.com/GKQTVxZ.png) <br> ![](https://i.imgur.com/PkiCFqS.png) <br> [![](https://i.imgur.com/9QZ57DV.png)](https://i.imgur.com/9QZ57DV.png) <br> - Here is a link to the trial license resource https://ngc.nvidia.com/resources/external-parabricks-trial-users:parabricks_free_trial 要使用你申請的 email 帳號，來登入到 nvidia (若沒帳號，則要註冊) 也就是，權限 `external-parabricks-trial-users` 綁定到 email 帳號 > You have been added to external-parabricks-trial-users organization. > You are now a member of the NGC private registry " external-parabricks-trial-users " > ![](https://i.imgur.com/cCx1gLi.png) > - Description > NVIDIA Clara Parabricks is a computational framework supporting genomics applications. It employs NVIDIA’s software stacks to build GPU accelerated libraries, pipelines, and reference application workflows for primary, secondary, and tertiary analysis. 沒權限，是底下這樣 ![](https://i.imgur.com/QkaFr1s.png) - [Here](https://forums.developer.nvidia.com/uploads/short-url/5kvnj7M9EiMH70vInNOHsj3GOiM.pdf) are the download instructions! https://forums.developer.nvidia.com/t/how-to-download-clara-parabricks-pipelines-trial-version/165217 - 直接點選下載 link (不work, 沒有link) - 從 File Browser 下載 (OK) - 透過 ngc 指令下載 (OK) - parabricks.tar.gz ``` ├── [ 793] Dockerfile_post ├── [2.4K] Dockerfile_post_extra_tools ├── [ 32K] EULA.txt ├── [ 24K] installer.py ├── [ 697] installMantaAndStrelka.sh ├── [ 181] license.bin ├── [ 698] singularity_post └── [1.6K] singularity_post_extra_tools ``` <br> <hr> <br> ## [補充] 在平台上安裝軟體 ### 安裝在 ESC4000 的資訊 ``` $ sudo python3 parabricks/installer.py ==================================== Installing Parabricks Final Selection: Install Directory: /opt/parabricks Install Version: v3.1.1 Install Container Type: docker Install Architecture: x86_64 registry.gitlab.com ==================================== ``` - GPU 記憶體不夠 - ESC4000 上，只有 11.1 GB - 實際在 TWCC/203.145.218.3 上，需要 11945 MiB <br> ### 安裝在 TWCC/203.145.218.3 的資訊 > ssh -i alpr_twcc_key.pem ubuntu@203.145.218.3 ``` ==================================== Installing Parabricks Final Selection: Install Directory: /opt/parabricks Install Version: v3.1.1 Install Container Type: docker Install Architecture: x86_64 registry.gitlab.com ==================================== Do you want to create a symlink to /usr/bin/pbrun ``` - 兩張 V100 - 當前 nvidia-docker 的資訊 ```bash $ nvidia-docker version NVIDIA Docker: 2.5.0 Client: Docker Engine - Community Version: 19.03.4 API version: 1.40 Go version: go1.12.10 Git commit: 9013bf583a Built: Fri Oct 18 15:54:09 2019 OS/Arch: linux/amd64 Experimental: false Server: Docker Engine - Community Engine: Version: 19.03.4 API version: 1.40 (minimum version 1.12) Go version: go1.12.10 Git commit: 9013bf583a Built: Fri Oct 18 15:52:40 2019 OS/Arch: linux/amd64 Experimental: false containerd: Version: 1.2.10 GitCommit: b34a5c8af56e510852c35414db4c1f4fa6172339 nvidia: Version: 1.0.0-rc8+dev GitCommit: 3e425f80a8c931f88e6d94a8c831b9d5aa481657 docker-init: Version: 0.18.0 GitCommit: fec3683 ``` <br> ### [一般安裝方式](https://www.nvidia.com/en-us/docs/parabricks/quickstart-guide/) ``` # Step 1: Unzip the package. $ tar -xzf parabricks.tar.gz # Step 2: Run the installer $ sudo ./parabricks/installer.py # Step 3: verify your installation. # This should display the parabricks version number: $ pbrun version ``` - **[trouble shooting]** docker: permission denied > WARNING: Error loading config file: /home/ubuntu/.docker/config.json: open /home/ubuntu/.docker/config.json: permission denied > ```bash $ ll /home/ubuntu/.docker/config.json -rw------- 1 root root 86 Oct 30 18:48 /home/ubuntu/.docker/config.json $ sudo chown $(id -u):$(id -g) /home/ubuntu/.docker/config.json $ ll /home/ubuntu/.docker/config.json -rw------- 1 ubuntu ubuntu 86 Oct 30 18:48 /home/ubuntu/.docker/config.json ``` - **[trouble shooting]** docker: permission denied > docker: Got permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock: Post http://%2Fvar%2Frun%2Fdocker.sock/v1.40/containers/create: dial unix /var/run/docker.sock: connect: permission denied. ```bash $ cat /etc/group | tail ... docker:x:999: ``` ```bash # 將目前使用者，加入到 docker 群組 # -a, --append # append the user to the supplemental GROUPS # mentioned by the -G option without removing # him/her from other groups # -G, --groups GROUPS # new list of supplementary GROUPS $ sudo usermod -aG docker $USER ``` ```bash ubuntu@alprworker-1203417-iaas:~/tj_tsai/parabricks/dataset$ cat /etc/group | tail ... docker:x:999:ubuntu ``` - **[trouble shooting]** docker image 消失了 ``` Unable to find image 'parabricks/release:v3.1.1' locally docker: Error response from daemon: pull access denied for parabricks/release, repository does not exist or may require 'docker login': denied: requested access to the resource is denied. See 'docker run --help'. ``` - 原因 ![](https://i.imgur.com/jUkndrt.png) - 只要執行的方式，是非法的 (就是自己帶參數進去) - 只要失敗 (比如路徑錯誤)，image 就會消失 (應該是被移除) - 查 docker images 就會找不到 <br> - installer.py 執行的指令 ``` docker login registry.gitlab.com -u pbuser -p dMwDDPMjGcyyzGZvu5dB docker pull registry.gitlab.com/pbuser/release/x86_64:v3.1.1 ``` 執行結果： ``` $ docker login registry.gitlab.com -u pbuser -p dMwDDPMjGcyyzGZvu5dB WARNING: Error loading config file: /home/ubuntu/.docker/config.json: open /home/ubuntu/.docker/config.json: permission denied WARNING! Using --password via the CLI is insecure. Use --password-stdin. WARNING! Your password will be stored unencrypted in /home/ubuntu/.docker/config.json. Configure a credential helper to remove this warning. See https://docs.docker.com/engine/reference/commandline/login/#credentials-store Login Succeeded $ docker pull registry.gitlab.com/pbuser/release/x86_64:v3.1.1 v3.1.1: Pulling from pbuser/release/x86_64 Digest: sha256:aeed0fc58ce8ff7c8dc03c8905752f794b0d33faa1e851d1bf785bf853de0e61 Status: Downloaded newer image for registry.gitlab.com/pbuser/release/x86_64:v3.1.1 registry.gitlab.com/pbuser/release/x86_64:v3.1.1 ``` 重新命名 docker image ``` $ sudo docker tag registry.gitlab.com/pbuser/release/x86_64:v3.1.1 parabricks/release:v3.1.1 ``` <br> ### [INSTALLING WITH SINGULARITY 3.0 OR HIGHER](https://www.nvidia.com/en-us/docs/parabricks/local-installation/) (這是透過 singularity) - 1) Log in to a machine with sudo access and singularity 3.0 or higher. - 2) To download the software: ``` $ wget -O parabricks.tar.gz " < DOWNLOAD_LINK > " ``` - 3) Unzip the package ``` $ tar -xvzf parabricks.tar.gz ``` - 4) Do a local installation: ``` $ mkdir localdir $ sudo ./parabricks/installer.py --install-location localdir --container singularity ``` - 5) Everything will be installed in localdir/parabricks folder. Tar this folder. ``` $ cd localdir $ tar -cvzf parabricks_install.tar.gz parabricks ``` - 6) and copy it to the node which will be used for testing and has singularity v3.x. - 7) Untar the tar.gz file in some <INSTALL_DIR>$ cd <INSTALL_DIR> ``` $ tar -xvzf parabricks_install.tar.gz ``` <br> ## [補充] 軟體授權 (license.bin) - [FAQS AND TROUBLESHOOTING](https://www.nvidia.com/en-us/docs/parabricks/quickstart-guide/faqs-and-troubleshooting/) > You might need to move the license to the correct path. It should be stored at **/opt/parabricks/license.bin** - #### Parabrick 工具如何提供「有授權」、「有期限」的憑證？ (它是如何控制能不能使用?) - 有一個二進位的授權，放在： ```/opt/parabricks/license.bin``` (類似憑證的概念) - 這個會過期，就會無法使用 pbrun 指令 要續約，就要找 Nvida <br> ## [補充] [官方測試資料](https://www.nvidia.com/en-us/docs/parabricks/quickstart-guide/) ```bash $ wget -O parabricks_sample.tar.gz \ "https://s3.amazonaws.com/parabricks.sample/parabricks_sample.tar.gz?Expires=1613069864&Signature=WxLeyitbvR%2B0rO4MX%2B0GohDw89g%3D&AWSAccessKeyId=AKIAJGDUNN2G2ZAH3Q3A" # To run the sample dataset: $ tar -xvzf parabricks_sample.tar.gz ``` ``` parabricks_sample ├── Data │   ├── sample_1.fq.gz (2.5G) │   └── sample_2.fq.gz (2.7G) └── Ref ├── Homo_sapiens_assembly38.dict ├── Homo_sapiens_assembly38.fasta (3.1G) ├── Homo_sapiens_assembly38.fasta.amb ├── Homo_sapiens_assembly38.fasta.ann ├── Homo_sapiens_assembly38.fasta.bwt ├── Homo_sapiens_assembly38.fasta.fai ├── Homo_sapiens_assembly38.fasta.pac ├── Homo_sapiens_assembly38.fasta.sa ├── Homo_sapiens_assembly38.known_indels.vcf.gz (59M) └── Homo_sapiens_assembly38.known_indels.vcf.gz.tbi (1.5M) 2 directories, 12 files ``` <br> ## [補充] 私人測試資料 - ### 台大基因案例子 ```bash pbrun fq2bam \ --ref /home/diatango_lin/tj_tsai/parabricks/dataset/D15780_S13_L001/human_g1k_v37_decoy.fasta \ --in-fq /home/diatango_lin/tj_tsai/parabricks/dataset/D15780_S13_L001/D15780_S13_L001_R1.fastq.gz \ /home/diatango_lin/tj_tsai/parabricks/dataset/D15780_S13_L001/D15780_S13_L001_R2.fastq.gz \ --out-bam /home/diatango_lin/tj_tsai/parabricks/dataset/D15780_S13_L001/out.bam ``` 縮短指令： ```bash dataset="/home/diatango_lin/tj_tsai/parabricks/dataset/D15780_S13_L001" pbrun fq2bam \ --ref $dataset/human_g1k_v37_decoy.fasta \ --in-fq $dataset/D15780_S13_L001_R1.fastq.gz \ $dataset/D15780_S13_L001_R2.fastq.gz \ --out-bam $dataset/out.bam ``` 執行結果： ``` Please visit https://www.nvidia.com/en-us/docs/parabricks/ for detailed documentation [Parabricks Options Mesg]: Checking argument compatibility [Parabricks Options Mesg]: Automatically generating ID prefix [Parabricks Options Mesg]: Read group created for /home/diatango_lin/tj_tsai/parabricks/dataset/D15780_S13_L001/D15780_S13_L001_R1.fastq.gz and /home/diatango_lin/tj_tsai/parabricks/dataset/D15780_S13_L001/D15780_S13_L001_R2.fastq.gz [Parabricks Options Mesg]: @RG\tID:000000000-C54LP.1\tLB:lib1\tPL:bar\tSM:sample\tPU:000000000-C54LP.1 ------------------------------------------------------------------------------ || Parabricks accelerated Genomics Pipeline || || Version v3.1.1 || || GPU-BWA mem, Sorting Phase-I || || Contact: Parabricks-Support@nvidia.com || ------------------------------------------------------------------------------ Not enough available memory for these GPUs... Please contact Parabricks-Support@nvidia.com if you are rightfully using the software but cannot run it. Please contact Parabricks-Support@nvidia.com for any questions. Exiting... Could not run fq2bam Exiting pbrun ... ``` - Not enough available memory for these GPUs... - 無法在 ESC4000 上跑，需在 TWCC/203.145.218.3 上執行 <br> ## [補充]```install.py``` 詳細執行過程 ```bash Downloading image $ docker login registry.gitlab.com -u pbuser -p dMwDDPMjGcyyzGZvu5dB $ docker pull registry.gitlab.com/pbuser/release/x86_64:v3.1.1 $ docker logout registry.gitlab.com Installing image $ docker tag registry.gitlab.com/pbuser/release/x86_64:v3.1.1 parabricks/release:v3.1.1 $ docker inspect --type=image parabricks/release:v3.1.1 $ docker rmi registry.gitlab.com/pbuser/release/x86_64:v3.1.1 Copying Scripts $ docker run --name=raw_run parabricks/release:v3.1.1 version $ docker cp raw_run:/parabricks/release-v3.1.1.tar.gz /opt/parabricks $ docker rm -f raw_run $ tar -xzf /opt/parabricks/release-v3.1.1.tar.gz -C /opt/parabricks $ /opt/parabricks/pbrun version ``` - image 儲存的地方，位於 /var/lib/docker 底下 ``` $ sudo find /var/lib/docker/ | grep v3.1 /var/lib/docker/overlay2/4f6......448/diff/parabricks/release-v3.1.1.tar.gz ``` ### 備份＆還原 image ```bash # save image #docker save registry.gitlab.com/pbuser/release/x86_64:v3.1.1 > parabricks_release-v3.1.1.tar.gz docker save -o parabricks_release-v3.1.1.tar.gz registry.gitlab.com/pbuser/release/x86_64:v3.1.1 # restore image docker load -i parabricks_release-v3.1.1.tar # rename image docker tag registry.gitlab.com/pbuser/release/x86_64:v3.1.1 parabricks/release:v3.1.1 ``` ## [補充] 上傳資料到 TWCC/203.145.218.3 的平均速度：873.96 (KB/s) ``` WES-EDA-013A_R1.fastq.gz 100% 2536MB 749.0KB/s 57:47 WES-EDA-013A_R2.fastq.gz 100% 2751MB 1.0MB/s 45:27 ``` ``` ├── [ 2658993692] WES-EDA-013A_R1.fastq.gz └── [ 2884234372] WES-EDA-013A_R2.fastq.gz ``` - 檔案大小，全部共 5543228064 bytes (=5.16 GB) - 上傳時間，全部共 1h:43m:14s (=6194s) - 透過外網，上傳資料到 TWCC 的平均速度： 5543228064 / 6194 / 1024 = 873.96 (KB/s) <br> ## [補充] v2/v3 版本差異性比較 ### image 差異性 ``` $ docker images | grep para parabricks/release v3.1.1 71c75a606a99 6 weeks ago 2.73GB parabricks/release v3.1.0 9bc71dfc4617 7 weeks ago 2.73GB parabricks/release v3.0.0 20d4f4cab175 5 months ago 2.62GB nvcr.io/hpc/parabricks v2.5.0 206e72b0a027 7 months ago 1.49GB ``` ### pbrun (in dcoker) 指令 help 差異性 ``` $ nvidia-docker run --rm parabricks/release:v3.1.1 pbrun ``` [![](https://i.imgur.com/1dYcDMn.png)](https://i.imgur.com/1dYcDMn.png)