[log] --cpu-only === ###### tags: `Parabricks-v3.5` ###### tags: `基因體`, `NVIDIA`, `Clara`, `Parabricks`, `二級分析` <br> [TOC] <br> ## `sudo python3 installer.py --cpu-only` - [INSTALLATION OPTIONS](https://docs.nvidia.com/clara/parabricks/v3.5/text/local_installation.html) - `--cpu-only` Install on a CPU server. No GPU accelerated tools will run with this option <br> ## 測試指令 ```bash= pbrun germline \ --ref parabricks_sample/Ref/Homo_sapiens_assembly38.fasta \ --in-fq dataset/WGS-LIS-AI018A_R1.fastq.gz \ dataset/WGS-LIS-AI018A_R2.fastq.gz \ --knownSites parabricks_sample/Ref/Homo_sapiens_assembly38.known_indels.vcf.gz \ --out-bam output.bam \ --out-variants output.vcf \ --out-recal-file report.txt \ --x3 ``` <br> ## 找不到 nvidia-smi ```= $ pbrun germline --ref parabricks_sample/Ref/Homo_sapiens_assembly38.fasta --in-fq dataset/WGS-LIS-AI018A_R1.fastq.gz dataset/WGS-LIS-AI018A_R2.fastq.gz --knownSites parabricks_sample/Ref/Homo_sapiens_assembly38.known_indels.vcf.gz --out-bam output.bam --out-variants output.vcf --out-recal-file report.txt --x3 Please visit https://docs.nvidia.com/clara/#parabricks for detailed documentation [pbutils.py] GetNumGPUs(): [Parabricks Options Mesg]: Automatically generating ID prefix [Parabricks Options Mesg]: Read group created for /uploads/workspace/dataset/WGS-LIS-AI018A_R1.fastq.gz and /uploads/workspace/dataset/WGS-LIS-AI018A_R2.fastq.gz [Parabricks Options Mesg]: @RG\tID:H3WFJDSXX.1\tLB:lib1\tPL:bar\tSM:sample\tPU:H3WFJDSXX.1 [pbutils.py] GetNumGPUs(): docker run -u=1000:1000 --rm -w=/uploads/workspace --net=host -v /opt/parabricks:/INSTALL/ -v /uploads/workspace/RMYVG0AE:/uploads/workspace/RMYVG0AE -v /uploads/workspace:/uploads/workspace -v /uploads/workspace/parabricks_sample/Ref:/uploads/workspace/parabricks_sample/Ref -v /uploads/workspace/dataset:/uploads/workspace/dataset parabricks/release:v3.5.0 fq2bam --ref /uploads/workspace/parabricks_sample/Ref/Homo_sapiens_assembly38.fasta --in-fq /uploads/workspace/dataset/WGS-LIS-AI018A_R1.fastq.gz /uploads/workspace/dataset/WGS-LIS-AI018A_R2.fastq.gz @RG\tID:H3WFJDSXX.1\tLB:lib1\tPL:bar\tSM:sample\tPU:H3WFJDSXX.1 --knownSites /uploads/workspace/parabricks_sample/Ref/Homo_sapiens_assembly38.known_indels.vcf.gz --out-bam /uploads/workspace/output.bam --out-recal-file /uploads/workspace/report.txt --memory-limit 55 --num-cpu-threads 0 --tmp-dir /uploads/workspace/RMYVG0AE --num-gpus 0 --x3 Please visit https://docs.nvidia.com/clara/#parabricks for detailed documentation Traceback (most recent call last): File "/parabricks/run_pipeline.py", line 7, in <module> sys.exit(PB.pb_main()) File "PB.pyx", line 1397, in PB.pb_main File "/parabricks/pbargs.py", line 1814, in getArgs return PBRun(sys.argv) File "/parabricks/pbargs.py", line 617, in __init__ self.runArgs = getattr(self, args.command)(argList) File "/parabricks/pbargs.py", line 682, in fq2bam self.addToParser(bsmb_parser_sysgroup, sysOptionGenerator().allOptions) File "/parabricks/pbargs.py", line 53, 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 87, in GetNumGPUs output = subprocess.check_output(["nvidia-smi", "-L"], universal_newlines=True) File "/usr/lib/python3.7/subprocess.py", line 411, in check_output **kwargs).stdout File "/usr/lib/python3.7/subprocess.py", line 488, in run with Popen(*popenargs, **kwargs) as process: File "/usr/lib/python3.7/subprocess.py", line 800, in __init__ restore_signals, start_new_session) File "/usr/lib/python3.7/subprocess.py", line 1551, in _execute_child raise child_exception_type(errno_num, err_msg, err_filename) FileNotFoundError: [Errno 2] No such file or directory: 'nvidia-smi': 'nvidia-smi' Could not run fq2bam as part of germline pipeline Exiting pbrun ... ``` <br> ## 偽裝 nvidia-smi 指令 ### Dockerfile ```dockerfile= FROM parabricks/release:v3.5.0 ADD nvidia-smi /usr/bin/nvidia-smi RUN chmod +x /usr/bin/nvidia-smi ``` nvidia-smi ``` #!/usr/bin/env python3 print('GPU 0: NVIDIA Tesla P100-PCIE-16GB (UUID: GPU-56989d15-2d15-c960-1729-2a713436bf5d)\n') ``` - 在主機的終端機中輸入 nvidia-smi，以獲取輸出結果 ### log ``` $ pbrun germline --ref parabricks_sample/Ref/Homo_sapiens_assembly38.fasta --in-fq dataset/WGS-LIS-AI018A_R1.fastq.gz dataset/WGS-LIS-AI018A_R2.fastq.gz --knownSites parabricks_sample/Ref/Homo_sapiens_assembly38.known_indels.vcf.gz --out-bam output.bam --out-variants output.vcf --out-recal-file report.txt --x3 Please visit https://docs.nvidia.com/clara/#parabricks for detailed documentation [pbutils.py] GetNumGPUs(): [Parabricks Options Mesg]: Automatically generating ID prefix [Parabricks Options Mesg]: Read group created for /uploads/workspace/dataset/WGS-LIS-AI018A_R1.fastq.gz and /uploads/workspace/dataset/WGS-LIS-AI018A_R2.fastq.gz [Parabricks Options Mesg]: @RG\tID:H3WFJDSXX.1\tLB:lib1\tPL:bar\tSM:sample\tPU:H3WFJDSXX.1 [pbutils.py] GetNumGPUs(): docker run -u=1000:1000 --rm -w=/uploads/workspace --net=host -v /opt/parabricks:/INSTALL/ -v /uploads/workspace/SK7PJ5GI:/uploads/workspace/SK7PJ5GI -v /uploads/workspace:/uploads/workspace -v /uploads/workspace/parabricks_sample/Ref:/uploads/workspace/parabricks_sample/Ref -v /uploads/workspace/dataset:/uploads/workspace/dataset parabricks/release:v3.5.0 fq2bam --ref /uploads/workspace/parabricks_sample/Ref/Homo_sapiens_assembly38.fasta --in-fq /uploads/workspace/dataset/WGS-LIS-AI018A_R1.fastq.gz /uploads/workspace/dataset/WGS-LIS-AI018A_R2.fastq.gz @RG\tID:H3WFJDSXX.1\tLB:lib1\tPL:bar\tSM:sample\tPU:H3WFJDSXX.1 --knownSites /uploads/workspace/parabricks_sample/Ref/Homo_sapiens_assembly38.known_indels.vcf.gz --out-bam /uploads/workspace/output.bam --out-recal-file /uploads/workspace/report.txt --memory-limit 55 --num-cpu-threads 0 --tmp-dir /uploads/workspace/SK7PJ5GI --num-gpus 0 --x3 Please visit https://docs.nvidia.com/clara/#parabricks for detailed documentation [Parabricks Options Mesg]: Checking argument compatibility [Parabricks Options Error]: --num-gpus cannot be set to 0 [Parabricks Options Error]: Run with -h to see help Could not run fq2bam as part of germline pipeline Exiting pbrun ... ```