一、 分析过程中用到的软件安装过程：
安装GATK：
# 从https://github.com/broadinstitute/gatk/releases/download/4.1.8.1/gatk-4.1.8.1.zip进行下载，然后解压安装： wget https://github.com/broadinstitute/gatk/releases/download/4.1.8.1/gatk-4.1.8.1.zip unzip gatk-4.1.8.1.zip cd gatk-4.1.8.1 ./gatk安装bwa-mem2：
# bwa-mem2比对速度优于bwa。 git clone --recursive https://github.com/bwa-mem2/bwa-mem2 cd bwa-mem2 make # 报错，需要安装g++和zlib apt install g++ apt install zlib1g-dev -y ./bwa-mem2安装fastp：
# fastp用于过滤原始测序数据。 conda install -c bioconda fastp安装samtools：
# samtools用于操作sam/bam文件。 conda install -c bioconda samtools安装 vcftools/bcftools：
# 用于操作vcf文件。 conda install -c bioconda vcftools bcftools
二、报错
bwa-mem2 make的时候报错：
报错详细信息：
(base) root@3eb13a5fb4e6:/home/software/bwa-mem2# make rm -f src/*.o libbwa.a; cd ext/safestringlib/ && make clean; make[1]: Entering directory '/home/software/bwa-mem2/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[1]: Leaving directory '/home/software/bwa-mem2/ext/safestringlib' make arch=sse41 EXE=bwa-mem2.sse41 CXX=g++ all make[1]: Entering directory '/home/software/bwa-mem2' g++ -c -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/fastmap.cpp -o src/fastmap.o make[1]: g++: No such file or directory make[1]: *** [Makefile:99: src/fastmap.o] Error 127 make[1]: Leaving directory '/home/software/bwa-mem2' make: *** [Makefile:105: multi] Error 2解决过程：
# 报错是因为系统里没有安装g++，所以没办法编译 apt-get update apt-get install -y build-essential # 安装后继续报错，日志内容如下： (base) root@3eb13a5fb4e6:/home/software/bwa-mem2# make rm -f src/*.o libbwa.a; cd ext/safestringlib/ && make clean; make[1]: Entering directory '/home/software/bwa-mem2/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[1]: Leaving directory '/home/software/bwa-mem2/ext/safestringlib' make arch=sse41 EXE=bwa-mem2.sse41 CXX=g++ all make[1]: Entering directory '/home/software/bwa-mem2' g++ -c -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/fastmap.cpp -o src/fastmap.o In file included from src/fastmap.cpp:39: src/fastmap.h:35:10: fatal error: zlib.h: No such file or directory 35 | #include <zlib.h> | ^~~~~~~~ compilation terminated. make[1]: *** [Makefile:99: src/fastmap.o] Error 1 make[1]: Leaving directory '/home/software/bwa-mem2' make: *** [Makefile:105: multi] Error 2 # 说明 缺少 zlib 开发库（压缩相关头文件），bwa-mem2 在编译时需要用到。 # 安装库 apt-get install -y zlib1g-dev
gatk的 Java 环境未正确配置
报错详细信息：
(base) root@961a4377e759:/home/Rmolle_calllsnp_work/Rmolle_results/bam_sort_bygatk# /home/softwore/gatk-4.1.8.1/gatk CreateSequenceDictionary -R /home/Rmolle_calllsnp_work/Rmolle_genome_GCA025413875/Rmolle_genomic_GCA_025413875.1.fna.gz -O Rmolle_genomic_GCA_025413875.1.dict Using GATK jar /home/softwore/gatk-4.1.8.1/gatk-package-4.1.8.1-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /home/softwore/gatk-4.1.8.1/gatk-package-4.1.8.1-local.jar CreateSequenceDictionary -R /home/Rmolle_calllsnp_work/Rmolle_genome_GCA025413875/Rmolle_genomic_GCA_025413875.1.fna.gz -O Rmolle_genomic_GCA_025413875.1.dict Traceback (most recent call last): File “/home/softwore/gatk-4.1.8.1/gatk”, line 479, in <module>main(sys.argv\[1:\]) File “/home/softwore/gatk-4.1.8.1/gatk”, line 152, in main runGATK(sparkRunner, sparkSubmitCommand, dryRun, gatkArgs, sparkArgs, javaOptions) File “/home/softwore/gatk-4.1.8.1/gatk”, line 328, in runGATK runCommand(cmd, dryrun) File “/home/softwore/gatk-4.1.8.1/gatk”, line 384, in runCommand check_call(cmd, env=gatk_env) File “/opt/conda/lib/python3.11/subprocess.py”, line 408, in check_call retcode = call(\*popenargs, \*\*kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File “/opt/conda/lib/python3.11/subprocess.py”, line 389, in call with Popen(\*popenargs, \*\*kwargs) as p: ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File “/opt/conda/lib/python3.11/subprocess.py”, line 1026, in **init** self.\_execute_child(args, executable, preexec_fn, close_fds, File “/opt/conda/lib/python3.11/subprocess.py”, line 1950, in \_execute_child raise child_exception_type(errno_num, err_msg, err_filename) FileNotFoundError: \[Errno 2\] No such file or directory: ‘java’</module>解决过程：
# 1.找到是未安装java还是环境未配置 java -version which java # 2.未安装 apt install openjdk-17-jdk -y # 3\. 设置 JAVA_HOME 和更新 PATH： # 查找 Java 安装路径（以 OpenJDK 为例） which java # 输出类似：/usr/bin/java → 实际路径为 /usr/lib/jvm/java-17-openjdk-amd64 # 编辑环境变量文件（如 ~/.bashrc 或 ~/.zshrc） echo ‘export JAVA_HOME=/usr/lib/jvm/java-17-openjdk-amd64’ >> ~/.bashrc echo ‘export PATH=$JAVA_HOME/bin:$PATH’ >> ~/.bashrc # 生效配置 source ~/.bashrc