pangenie¶

PanGenie是一种输入数据为短读型的基因分型器，通过考虑已知单倍型的信息（通过图中的路径表示）可有效计算泛基因组图中以气泡表示的变异的基因型。

可用版本¶

平台	版本	构建方式	路径
思源一号	v2.0.0	容器	/dssg/share/imgs/pangenie/pangenie_v2.0.0.sif
pi2.0	v2.0.0	容器	/lustre/share/img/x86/pangenie/pangenie_v2.0.0.sif
ARM	v2.0.0	容器	/lustre/share/img/arm/pangenie/pangenie_v2.0.0.sif

算例路径¶

平台	路径
思源一号	/dssg/share/sample/pangenie
pi 2.0	/lustre/share/samples/pangenie
ARM	/lustre/share/samples/pangenie

思源一号 PanGenie¶

首先拷贝数据到本地¶

cd
mkdir pangenie
cp -r /dssg/share/sample/pangenie/* ./

然后在数据目录下提交如下脚本¶

#!/bin/bash
#SBATCH --job-name=pangenie_sy
#SBATCH --partition=64c512g
#SBATCH -N 1
#SBATCH --ntasks-per-node=1
#SBATCH --output=%j.out
#SBATCH --error=%j.err

IMAGE=/dssg/share/imgs/pangenie/pangenie_v2.0.0.sif
singularity exec $IMAGE PanGenie -i test-reads.fa -r test-reference.fa -v test-variants.vcf -o test -e 100000

π2.0 PanGenie¶

首先，拷贝数据到本地¶

cd
mkdir pangenie
cp -r /lustre/share/samples/pangenie/* ./

然后，在数据目录下提交如下脚本¶

#!/bin/bash
#SBATCH --job-name=pangenie_x86
#SBATCH --partition=small
#SBATCH -N 1
#SBATCH --ntasks-per-node=1
#SBATCH --output=%j.out
#SBATCH --error=%j.err

IMAGE=/lustre/share/img/x86/pangenie/pangenie_v2.0.0.sif
singularity exec $IMAGE PanGenie -i test-reads.fa -r test-reference.fa -v test-variants.vcf -o test -e 100000

ARM PanGenie¶

首先将数据拷贝到本地¶

cd
mkdir pangenie
cp -r /lustre/share/samples/pangenie/* ./

然后提交如下作业脚本¶

#!/bin/bash
#SBATCH --job-name=pangenie_arm
#SBATCH --partition=arm128c256g
#SBATCH -N 1
#SBATCH --ntasks-per-node=1
#SBATCH --output=%j.out
#SBATCH --error=%j.err

IMAGE=/lustre/share/img/arm/pangenie/pangenie_v2.0.0.sif
singularity exec $IMAGE PanGenie -i test-reads.fa -r test-reference.fa -v test-variants.vcf -o test -e 100000

PanGenie运行结果¶

PanGenie-思源一号¶

###### Summary ######
time spent reading input files: 0.532767 sec
time spent counting kmers:      0.116464 sec
time spent selecting paths:     0.000311676 sec
time spent determining unique kmers:    0.00101096 sec
time spent genotyping chromosome chr1:  0.0527584
total running time:     0.703721 sec
total wallclock time: 0.702943 sec
Total maximum memory usage: 0.024004 GB

PanGenie-pi 2.0¶

###### Summary ######
time spent reading input files: 0.0779914 sec
time spent counting kmers:      0.107329 sec
time spent selecting paths:     0.00195029 sec
time spent determining unique kmers:    0.0354376 sec
time spent genotyping chromosome chr1:  0.0532523
total running time:     0.276735 sec
total wallclock time: 0.274615 sec
Total maximum memory usage: 0.015336 GB

PanGenie-ARM¶

###### Summary ######
time spent reading input files: 0.00858966 sec
time spent counting kmers:      0.0387264 sec
time spent selecting paths:     0.0010025 sec
time spent determining unique kmers:    0.00505522 sec
time spent genotyping chromosome chr1:  0.215358
total running time:     0.270459 sec
total wallclock time: 0.268968 sec
Total maximum memory usage: 0.0128 GB

参考资料¶

PanGenie GitHub https://github.com/eblerjana/pangenie

最后更新: 2024 年 11 月 22 日