【6.1】nextNEOpi--新抗原的预测

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一、安装

conda clean -i conda config –show

conda env create -f assets/nextNEOpi.yml

四、报错：

4.1 报错1

WARN: =============================================================================
  There is a problem with your Conda configuration!

  You will need to set-up the conda-forge and bioconda channels correctly.
  Please refer to https://bioconda.github.io/user/install.html#set-up-channels
  NB: The order of the channels matters!

(base) [sam@c01 nextNEOpi]$ cat  ~/.condarc
channels:
  - bioconda
  - conda-forge
  - defaults

更新为：

channels:
  - defaults
show_channel_urls: true
default_channels:
  - https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
  - https://mirrors.bfsu.edu.cn/anaconda/pkgs/free
  - https://mirrors.bfsu.edu.cn/anaconda/pkgs/r
  - https://mirrors.bfsu.edu.cn/anaconda/pkgs/pro
  - https://mirrors.bfsu.edu.cn/anaconda/pkgs/msys2
custom_channels:
  conda-forge: https://mirrors.bfsu.edu.cn/anaconda/cloud
  msys2: https://mirrors.bfsu.edu.cn/anaconda/cloud
  bioconda: https://mirrors.bfsu.edu.cn/anaconda/cloud
  menpo: https://mirrors.bfsu.edu.cn/anaconda/cloud
  pytorch: https://mirrors.bfsu.edu.cn/anaconda/cloud
  simpleitk: https://mirrors.bfsu.edu.cn/anaconda/cloud

命令行：

conda clean -i
conda config --show

conda env create -f assets/nextNEOpi.yml

4.2 报错

curl -L -o gatk-3.8.tar.bz2 https://anaconda.org/bioconda/gatk/3.8/download/noarch/gatk-3.8-hdfd78af_11.tar.bz2 && \

tar -xjf gatk-3.8.tar.bz2 opt/gatk-3.8/GenomeAnalysisTK.jar &&
gatk-register opt/gatk-3.8/GenomeAnalysisTK.jar &&
touch gatk3_install.ok

解决：

conda install -c conda-forge -c bioconda gatk

接着报错：

Error: A JNI error has occurred, please check your installation and try agai

(nextNEOpi) [sam@c01 nextNEOpi]$ which java
/data/software/anaconda3/envs/nextNEOpi/bin/java
(nextNEOpi) [sam@c01 nextNEOpi]$ which javac
/data/software/anaconda3/envs/nextNEOpi/bin/javac
(nextNEOpi) [sam@c01 nextNEOpi]$ mv /data/software/anaconda3/envs/nextNEOpi/bin/java /data/software/anaconda3/envs/nextNEOpi/bin/java.bak
(nextNEOpi) [sam@c01 nextNEOpi]$ which java
/usr/bin/java
(nextNEOpi) [sam@c01 nextNEOpi]$ mv /data/software/anaconda3/envs/nextNEOpi/bin/javac /data/software/anaconda3/envs/nextNEOpi/bin/javac.bak

解决办法（这里的问题，其实nextflow的版本问题，高版本不支持低版本的java）：

(nextNEOpi) [sam@c01 nextNEOpi]$ ln -s /usr/bin/java  /data/software/anaconda3/envs/nextNEOpi/bin/java
(nextNEOpi) [sam@c01 nextNEOpi]$ ln -s /usr/bin/javac  /data/software/anaconda3/envs/nextNEOpi/bin/javac

接着报错：

(nextNEOpi) [sam@c01 nextNEOpi]$ gatk
GATK jar file not found. Have you run "gatk-register"?

解决办法： 需要注册gatk

curl -L -o gatk-3.8.tar.bz2 https://anaconda.org/bioconda/gatk/3.8/download/noarch/gatk-3.8-hdfd78af_11.tar.bz2
gatk-register  gatk-3.8-hdfd78af_11.tar.bz2

最后如果用java 11, gatk启动不了。 如果用java 8 ，nextflow启动不了。不得已，要改nextflow的版本。

rror: A JNI error has occurred, please check your installation and try again

这里的问题是，nextflow 23的版本太高，需要Java11。 我尝试安装 nextflow 20 版本，又提示报错：

Unknown method toRealPath on ConfigObject type

修改文件：

wget -c  https://get.nextflow.io 
mv index.html nextflow_install.bash

修改 nextflow_install.bash 中版本， 然后改成 22.04.0 一定要卡在这个版本 接着：

bash  nextflow_install.bash
mv nextflow_install.bash nextflow
chmod 777 nextflow

这个nextflow就可以用了

4.4 cnvkit 报错

(nextNEOpi) [sam@c01 nextNEOpi]$ conda install -c bioconda cnvkit=0.9.9
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: / ^[\
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abor|
failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versionsThe following specifications were found to be incompatible with your system:

  - feature:/linux-64::__glibc==2.28=0
  - feature:|@/linux-64::__glibc==2.28=0

Your installed version is: 2.28

解决办法：

调整了cnkit的安装顺序

4.5 error executing process > ‘install_IGS (install IGS)’

报错：

Caused by:
  Process `install_IGS (install IGS)` terminated with an error exit status (52)

手动执行（因为网速的问题）

Command executed:

  mkdir -p /home/sam/project/neoantigen/lib/nextNEOpi/nextNEOpi/work/IGS && \
  curl -sLk https://github.com/vincentlaboratories/neoag/raw/master/NeoAg_immunogenicity_predicition_GBM.R -o /home/sam/project/neoantigen/lib/nextNEOpi/nextNEOpi/work/IGS/NeoAg_immunogenicity_predicition_GBM.R && \
  
  curl -sLk https://github.com/vincentlaboratories/neoag/raw/master/Final_gbm_model.rds -o /home/sam/project/neoantigen/lib/nextNEOpi/nextNEOpi/work/IGS/Final_gbm_model.rds && \
  
  patch -p0 /home/sam/project/neoantigen/lib/nextNEOpi/nextNEOpi/work/IGS/NeoAg_immunogenicity_predicition_GBM.R /home/sam/project/neoantigen/lib/nextNEOpi/nextNEOpi/assets/NeoAg_immunogenicity_predicition_GBM.patch && \
  
  chmod +x /home/sam/project/neoantigen/lib/nextNEOpi/nextNEOpi/work/IGS/NeoAg_immunogenicity_predicition_GBM.R  && \
  echo "OK" > .igs_install_ok.chck && \
  
  cp -f .igs_install_ok.chck /home/sam/project/neoantigen/lib/nextNEOpi/nextNEOpi/work/.igs_install_ok.chck

4.6 IEDB安装失败

CWD=`pwd`
cd /opt/iedb/
rm -f IEDB_MHC_I-3.1.2.tar.gz
wget https://downloads.iedb.org/tools/mhci/3.1.2/IEDB_MHC_I-3.1.2.tar.gz
tar -xzvf IEDB_MHC_I-3.1.2.tar.gz
cd mhc_i
bash -c "./configure"
cd /opt/iedb/
rm -f IEDB_MHC_I-3.1.2.tar.gz

rm -f IEDB_MHC_II-3.1.6.tar.gz
wget https://downloads.iedb.org/tools/mhcii/3.1.6/IEDB_MHC_II-3.1.6.tar.gz
tar -xzvf IEDB_MHC_II-3.1.6.tar.gz
cd mhc_ii
bash -c "python ./configure.py"
cd /opt/iedb/
rm IEDB_MHC_II-3.1.6.tar.gz

export MHCFLURRY_DATA_DIR=/opt/mhcflurry_data
mhcflurry-downloads fetch    ## 这一个太夸张了，数据太大，一直下载失败，需要手动下载

cd $CWD
echo "OK" > .iedb_install_ok.chck

4.7 VEP cache下载失败，手动下载

singularity exec /home/sam/project/neoantigen/lib/nextNEOpi/nextNEOpi/singularity/ensembl-vep:106.1--pl5321h4a94de4_0 vep_install -a cf -s homo_sapiens -y GRCh38 -c /home/sam/project/neoantigen/lib/nextNEOpi/nextNEOpi/resources/databases/vep_cache  --CACHE_VERSION 106  --CONVERT 2  

singularity exec /home/sam/project/neoantigen/lib/nextNEOpi/nextNEOpi/singularity/ensembl-vep:106.1--pl5321h4a94de4_0 vep_install  -a p -c /home/sam/project/neoantigen/lib/nextNEOpi/nextNEOpi/resources/databases/vep_cache --CACHE_VERSION 106  --PLUGINS all 2

接着报错：

Available plugins: AncestralAllele,Blosum62,CADD,CAPICE,CSN,Carol,ClinPred,Condel,Conservation,DisGeNET,Downstream,Draw,ExAC,ExACpLI,FATHMM,FATHMM_MKL,FlagLRG,FunMotifs,G2P,GO,GeneSplicer,Gwava,HGVSIntronOffset,IntAct,LD,LOEUF,LOVD,LoF,LoFtool,LocalID,MPC,MTR,Mastermind,MaxEntScan,NMD,NearestExonJB,NearestGene,PON_P2,Phenotypes,PostGAP,PrimateAI,ProteinSeqs,REVEL,ReferenceQuality,SameCodon,SingleLetterAA,SpliceAI,SpliceRegion,StructuralVariantOverlap,SubsetVCF,TSSDistance,dbNSFP,dbscSNV,gnomADc,miRNA,neXtProt,satMutMPRA


  - installing "Gwava"
Use of uninitialized value in numeric eq (==) at /usr/local/lib/perl5/core_perl/HTTP/Tiny.pm line 615.
Use of uninitialized value in numeric eq (==) at /usr/local/lib/perl5/core_perl/HTTP/Tiny.pm line 615.
ERROR: Failed last resort of using HTTP::Tiny to download ftp://ftp.sanger.ac.uk:21/pub/resources/software/gwava/v1.0/VEP_plugin/Gwava.pm

解决办法：

重新下载

参考资料

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