---
# System prepended metadata

title: '[log] germline: WGS + AWS: g4dn.xlarge (T4 + 4vCPU + 16GB)'
tags: [Clara, Parabricks-v3.8, 基因體, 二級分析, NVIDIA, Parabricks]

---

[log] germline: WGS + AWS: g4dn.xlarge (T4 + 4vCPU + 16GB)
===
###### tags: `Parabricks-v3.8`
###### tags: `基因體`, `NVIDIA`, `Clara`, `Parabricks`, `二級分析`

:::danger
:no_entry_sign: 此規格 **g4dn.xlarge (T4 + 4vCPU + 16GB)**，跑不起來
:::

<br>

[TOC]

<br>

## 硬體資源：EC2 / g4dn.xlarge
> 查閱方式：[[HackMD] AWS / 容器執行個體(EC2) / EC2 / g4dn.xlarge](https://hackmd.io/QavypnMBRoW8P9aH4gw8FA#EC2--g4dnxlarge)

[![](https://i.imgur.com/N6fauHL.png)](https://i.imgur.com/N6fauHL.png)

### GPU
- GPU 0: Tesla T4 (15360MiB)

### CPU
- Intel® Xeon® Platinum 8259CL CPU @ 2.50GHz
- 1(插槽) x 2(核/插槽) x 2(超執行緒/核) = 4條執行緒 (4vCPU)

### RAM
- 16GB

<br>

<hr>

<br>

## script 
```bash=
# cmd: sh germline.sh 2>&1 | tee germline.sh.log &

date && start_time=`date +%s` && echo "start_time:" $start_time

pbrun germline \
  --ref parabricks_sample/Ref/Homo_sapiens_assembly38.fasta \
  --in-fq \
    datasets/WGS-LIS-AI018A_R1.fastq.gz \
    datasets/WGS-LIS-AI018A_R2.fastq.gz \
  --knownSites parabricks_sample/Ref/Homo_sapiens_assembly38.known_indels.vcf.gz \
  --out-bam        output/output.bam \
  --out-variants   output/output.vcf \
  --out-recal-file output/report.txt; \
  echo "exit code:" $!; \
  echo "Done!"

date && end_time=`date +%s` && echo "end_time:" $end_time

total=$((end_time - start_time))
time_h=$((total/3600))
time_m=$(( (total - time_h*3600) / 60 ))
time_s=$(( total - time_h*3600 - time_m*60 ))
echo "Total time: ${time_h}h ${time_m}m ${time_s}s"
```

<br>

<hr>

<br>

## Log
> **g4dn.xlarge (T4 + 4vCPU + 16GB)**
```
$ Thu Mar 17 02:40:15 UTC 2022
start_time: 1647484815
Please visit https://docs.nvidia.com/clara/#parabricks for detailed documentation


[Parabricks Options Mesg]: Automatically generating ID prefix
[Parabricks Options Mesg]: Read group created for /workspace/datasets/WGS-LIS-AI018A_R1.fastq.gz and
/workspace/datasets/WGS-LIS-AI018A_R2.fastq.gz
[Parabricks Options Mesg]: @RG\tID:H3WFJDSXX.1\tLB:lib1\tPL:bar\tSM:sample\tPU:H3WFJDSXX.1

[Parabricks Options Mesg]: Checking argument compatibility
[Parabricks Options Mesg]: Read group created for /workspace/datasets/WGS-LIS-AI018A_R1.fastq.gz and
/workspace/datasets/WGS-LIS-AI018A_R2.fastq.gz
[Parabricks Options Mesg]: @RG\tID:H3WFJDSXX.1\tLB:lib1\tPL:bar\tSM:sample\tPU:H3WFJDSXX.1
[PB Info 2022-Mar-17 02:40:15] Logger not initialized! 
[PB Info 2022-Mar-17 02:40:15] ------------------------------------------------------------------------------
[PB Info 2022-Mar-17 02:40:15] ||                 Parabricks accelerated Genomics Pipeline                 ||
[PB Info 2022-Mar-17 02:40:15] ||                              Version 3.7.0-1                             ||
[PB Info 2022-Mar-17 02:40:15] ||                       GPU-BWA mem, Sorting Phase-I                       ||
[PB Info 2022-Mar-17 02:40:15] ||                  Contact: Parabricks-Support@nvidia.com                  ||
[PB Info 2022-Mar-17 02:40:15] ------------------------------------------------------------------------------
gpg: keyblock resource '/home/ubuntu/.gnupg/pubring.kbx': Permission denied
[PB Info 2022-Mar-17 02:40:16] Logger already initialized, continuing with current settings.
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[PB Warning 2022-Mar-17 02:41:00][ParaBricks/src/pbOpts.cu:316] 

WARNING
The system has 15 GB, however recommended RAM with 1 GPU is 64 GB.
The run might not finish or might have less than expected performance.

[PB Warning 2022-Mar-17 02:41:00][ParaBricks/src/pbOpts.cu:325] 

WARNING
The system has 4 threads, however recommended number of threads with 1 GPU is 16.
The run might not finish or might have less than expected performance.

[PB Info 2022-Mar-17 02:41:00] GPU-BWA mem
[PB Info 2022-Mar-17 02:41:00] ProgressMeter	Reads		Base Pairs Aligned
[PB Info 2022-Mar-17 02:43:34] 5033176		760000000
Killed
For technical support visit https://docs.nvidia.com/clara/parabricks/3.7.0/index.html#how-to-get-help
Exiting...


Could not run fq2bam as part of germline pipeline
Exiting pbrun ...
Thu Mar 17 02:44:56 UTC 2022
end_time: 1647485096
Total time: 0h 4m 41s
```
:::warning
:warning: **WARNING**
The system has 15 GB, however recommended RAM with 1 GPU is 64 GB.
The run might not finish or might have less than expected performance.
:::
:::warning
:warning: **WARNING**
The system has 4 threads, however recommended number of threads with 1 GPU is 16.
The run might not finish or might have less than expected performance.
:::


<br>

## 出現過的 exit code
```
Killed
For technical support visit https://docs.nvidia.com/clara/parabricks/3.7.0/index.html#how-to-get-help
Exiting...

Could not run fq2bam as part of germline pipeline
Exiting pbrun ...
exit code: 2265
```
```
Killed
For technical support visit https://docs.nvidia.com/clara/parabricks/3.7.0/index.html#how-to-get-help
Exiting...

Could not run fq2bam as part of germline pipeline
Exiting pbrun ...
exit code: 3479
```

Ctrl+C 中斷：
```
^CExiting...For technical support visit https://docs.nvidia.com/clara/parabricks/3.7.0/index.html#how-to-get-help
[PB Error 2022-Mar-17 04:38:17][-unknown-:0] Received signal: 2
For technical support visit https://docs.nvidia.com/clara/parabricks/3.7.0/index.html#how-to-get-help[PB Error 2022-Mar-17 04:38:18][-unknown-:0] [PB Error 2022-Mar-17 04:38:20][-unknown-:0] Received signal: 2
For technical support visit https://docs.nvidia.com/clara/parabricks/3.7.0/index.html#how-to-get-helpReceived signal: 2
For technical support visit https://docs.nvidia.com/clara/parabricks/3.7.0/index.html#how-to-get-help, exiting.
, exiting.
, exiting.
Traceback (most recent call last):
  File "/usr/local/parabricks/run_pipeline.py", line 7, in <module>
    sys.exit(PB.pb_main())
  File "PB.pyx", line 2169, in PB.pb_main
  File "PB.pyx", line 394, in PB.runfq2bam
  File "PB.pyx", line 131, in PB.RunBinary
  File "/usr/lib/python3.7/subprocess.py", line 341, in call
    return p.wait(timeout=timeout)
  File "/usr/lib/python3.7/subprocess.py", line 1019, in wait
    return self._wait(timeout=timeout)
  File "/usr/lib/python3.7/subprocess.py", line 1653, in _wait
    (pid, sts) = self._try_wait(0)
  File "/usr/lib/python3.7/subprocess.py", line 1611, in _try_wait
    (pid, sts) = os.waitpid(self.pid, wait_flags)
  File "PB.pyx", line 54, in PB.signal_handler
  File "PB.pyx", line 50, in PB.exitFunction
  File "PB.pyx", line 54, in PB.signal_handler
  File "PB.pyx", line 49, in PB.exitFunction
  File "PB.pyx", line 54, in PB.signal_handler
  File "PB.pyx", line 49, in PB.exitFunction
RuntimeError: reentrant call inside <_io.BufferedWriter name='<stdout>'>

Exiting pbrun ...
exit code: 3479
```
