1 使用conda安装EVM。conda源的evidencemodeler 不是作者编译上传的，所以pasa的依赖和库都不在，如果是重新创建环境安装EVM的话，需要安装这俩PASA，ParaFly。
conda install -c conda-forge -c bioconda pasa
conda install -c conda-forge -c bioconda evidencemodeler
conda install -c conda-forge -c bioconda parafly
2 conda在使用的时候不会把evidencemodeler 的脚本放入环境变量，而且可能无法访问pasa对应的perl库。需要把对应conda下脚本的路径放入环境变量，以及给perl库加权限，同样放入环境变量。
export PATH="/path/to/miniconda3/envs/EVM/opt/evidencemodeler-2.1.0/EvmUtils/:$PATH"
export PATH="/path/to/miniconda3/envs/EVM/opt/evidencemodeler-2.1.0/EvmUtils/misc/:$PATH"
cd ~/miniconda3/envs/EVM/opt/pasa-2.5.3/PerlLib
chmod 777 *.pm
chmod 777 ./*/*.pm
export PATH="/path/to/miniconda3/envs/EVM/opt/pasa-2.5.3/PerlLib:$PATH"
3 这样EVM就能顺利运行了
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报错1 缺少PASA环境和对应的pm库，需要按照如上步骤安好PASA和ParaFly，并把对应的库加权限放环境。
FAILURE:[4400] /home/xfm/miniconda3/envs/EVM/bin/EvmUtils/evidence_modeler.pl -G cy20.afterhic.fasta.masked -g Abinits.gff3 -w /home/xfm/bio_data/09.EVM/cy/weights.txt -e transcript_alignments.gff3 -p gemoma.evm.format.gff3 --min_intron_length 20 --terminal_intergenic_re_search 10000 --exec_dir JY.EVM.partitions/scaffold_5/scaffold_5_16110001-16210000 > JY.EVM.partitions/scaffold_5/scaffold_5_16110001-16210000/evm.out 2> JY.EVM.partitions/scaffold_5/scaffold_5_16110001-16210000/evm.out.log
We are sorry, commands in file: [JY.EVM.failed_cmds] failed. :-(
Error, cmd: /home/xfm/miniconda3/envs/EVM/bin/plugins/ParaFly/bin/ParaFly -c JY.EVM.partitions.evm_cmds -CPU 14 -vv -max_retry 1 -failed_cmds JY.EVM.failed_cmds -shuffle died with ret 256 No such file or directory at /home/xfm/miniconda3/envs/EVM/bin/PerlLib/Pipeliner.pm line 187.
Pipeliner::run(Pipeliner=HASH(0x564084ce25c8)) called at /home/xfm/miniconda3/envs/EVM/bin/EVidenceModeler line 365
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报错2 这部分报错是因为gff格式不符合EVM要求，需要使用EVm的脚本处理对应文件。
Valid prediction for GeneMark.hmm_scaffold_1-MSTRG.13.1
Valid prediction for Augustus_model.g12046.t1
-loading the search evidence (protein and EST search results, strand: +)error, no chainID in attributes Parent=SFa_chr5.g08357.m1_R3 of line scaffold_1 GeMoMa CDS 6411 6521 . + 0 Parent=SFa_chr5.g08357.m1_R3
