●   报错1

●  报错内容：

●  mv: cannot stat ‘/path/genemark_hintsfile.gff.rnaseq.tmp’: No such file or directory

●  ERROR in file /path/braker.pl at line 6295

●  Failed to execute: mv /path/braker/genemark_hintsfile.gff.rnaseq.tmp /path/genemark_hintsfile.gff

●  解决措施：

●  重新提交作业

●   报错2

●  报错内容：

●   ERROR: in file /your_path/braker.pl at line 4590

●  /your_path/bin/../config/species/species_name already exists

●  解决措施：

●  删除已构建的物种模型目录：rm -r /your_path/bin/../config/species/Fv

●   报错3

●  报错内容：

●  braker之外的依赖包路径找不到，比如：

●  # WARNING: Guessing the location of $GENEMARK_PATH failed.

            ●  ERROR: in file /your_path/bin/braker.pl at line 2172

            ●  $GENEMARK_PATH not set!

●  解决措施：

●  在脚本中手动添加各种依赖的绝对路径，export

●   export GENEMARK_PATH=/your_path/gmes_linux_64/

●   export BAMTOOLS_PATH=/your_path/envs/annotation/bin/

●   export SAMTOOLS_PATH=/your_path/envs/annotation/bin/

●   export PYTHON3_PATH=/your_path/envs/annotation/bin/

●   export DIAMOND_PATH=/your_path/envs/annotation/bin/

●   export CDBTOOLS_PATH=/your_path/cdbtools/

●   export AUGUSTUS_BIN_PATH=/your_path/envs/annotation/bin/../config/../bin

●   export AUGUSTUS_SCRIPTS_PATH=/your_path/envs/annotation/bin/

●   export ALIGNMENT_TOOL_PATH=/your_path/envs/annotation/bin/

●   export AUGUSTUS_CONFIG_PATH=/your_path/envs/annotation/config/

●   export PATH=/your_path/envs/annotation/bin/:$PATH

●   报错4

●  报错内容：

●  WARNING: Detected whitespace in fasta header of file /your_path/Fv/Fv.fasta.maksed.

●   This may later on cause problems! The pipeline will create a new file without spaces or "|" characters and a genome_header.map file to look up the old and new headers.

●  This message will be suppressed from now on!

●  解决措施：删除fasta文件（参考基因组或蛋白pep文件）中的空格，且不能使用管道符，可以使用下划线

●   报错5

●  报错内容：

●  Failed to create new species with new_species.pl, check write permissions in /your_path/envs/annotation/bin/../config/species directory!

●  Command was perl /your_path/bin/new_species.pl --species=species_name --AUGUSTUS_CONFIG_PATH=/your_path/bin/../config 1> /dev/null 2>/your_path/braker/your_species/braker/errors/new_species.stderr

●  解决措施：拷贝braker的species目录下的generic到自己的目录下

●   报错6

●  报错内容：The hints file is empty. Maybe the genome and the RNA-seq file do not belong together.

●  解决措施：检查softmasked基因组文件和sam文件的ID是否对应

●   提示：

●  cpu官方建议设置为48核心

●  expert argument：--rounds

●  尽可能多选一些同源蛋白，转录组比对的bam文件