报错所有信息：NOTICE: the --polish argument is set ON automatically (use --nopolish to change this behavior)

NOTICE: Running with system command <convert2annovar.pl  -includeinfo -allsample -withfreq -format vcf4 /work/bdorsalis/4.snp_indel/var_qc/all.clean.snp.vcf.gz > /work/bdorsalis/5.var_ann/test/snp.avinput>

NOTICE: Finished reading 840 lines from VCF file

NOTICE: A total of 224 locus in VCF file passed QC threshold, representing 224 SNPs (152 transitions and 72 transversions) and 0 indels/substitutions

NOTICE: Finished writing allele frequencies based on 1344 SNP genotypes (912 transitions and 432 transversions) and 0 indels/substitutions for 6 samples

NOTICE: Running with system command </share/work/biosoft/annovar/latest/table_annovar.pl /work/bdorsalis/5.var_ann/test/snp.avinput /work/bdorsalis/ref/test -buildver unknown -outfile /work/bdorsalis/5.var_ann/test/snp -remove -protocol refGene -operation g -nastring . -otherinfo>

NOTICE: the --polish argument is set ON automatically (use --nopolish to change this behavior)

-----------------------------------------------------------------

NOTICE: Processing operation=g protocol=refGene

NOTICE: Running with system command <annotate_variation.pl -geneanno --neargene 1000  -buildver unknown -dbtype refGene -outfile /work/bdorsalis/5.var_ann/test/snp.refGene -exonsort -nofirstcodondel /work/bdorsalis/5.var_ann/test/snp.avinput /work/bdorsalis/ref/test>

NOTICE: Output files are written to /work/bdorsalis/5.var_ann/test/snp.refGene.variant_function, /work/bdorsalis/5.var_ann/test/snp.refGene.exonic_variant_function

NOTICE: Reading gene annotation from /work/bdorsalis/ref/test/unknown_refGene.txt ... Done with 34330 transcripts (including 4228 without coding sequence annotation) for 16570 unique genes

NOTICE: Processing next batch with 224 unique variants in 224 input lines

NOTICE: Reading FASTA sequences from /work/bdorsalis/ref/test/unknown_refGeneMrna.fa ... Done with 77 sequences

WARNING: A total of 151 sequences will be ignored due to lack of correct ORF annotation

NOTICE: Running with system command <coding_change.pl  /work/bdorsalis/5.var_ann/test/snp.refGene.exonic_variant_function.orig /work/bdorsalis/ref/test/unknown_refGene.txt /work/bdorsalis/ref/test/unknown_refGeneMrna.fa -alltranscript -out /work/bdorsalis/5.var_ann/test/snp.refGene.fa -newevf /work/bdorsalis/5.var_ann/test/snp.refGene.exonic_variant_function>

Error: invalid record found in exonic_variant_function file (exonic format error): <line3       synonymous SNV  gene-LOC105223489:rna-XM_049455802.1#NC_064303.1#9685699:exon4:c.T1656C:p.F552F,gene-LOC105223489:rna-XM_049455807.1#NC_064303.1#9685699:exon5:c.T1656C:p.F552F NC_064303.1     9687053 9687053 A       G      0.8      404.75  5       NC_064303.1     9687053 .       A       G       404.75 PASS     AC=8;AF=0.800;AN=10;BaseQRankSum=-0.581;DP=19;ExcessHet=3.5218;FS=0.000;MLEAC=8;MLEAF=0.800;MQ=60.00;MQRankSum=0.000;QD=21.30;ReadPosRankSum=-0.185;SOR=0.368   GT:AD:DP:GQ:PL  1/1:0,3:3:9:59,9,0      1/1:0,4:4:12:133,12,0   ./.:.:.:.:.     0/1:1,2:3:33:40,0,33    0/1:2,2:4:37:37,0,37    1/1:0,5:5:15:141,15,0> at /share/work/biosoft/annovar/latest/coding_change.pl line 77, <EVF> line 1.

Error running system command: <coding_change.pl  /work/bdorsalis/5.var_ann/test/snp.refGene.exonic_variant_function.orig /work/bdorsalis/ref/test/unknown_refGene.txt /work/bdorsalis/ref/test/unknown_refGeneMrna.fa -alltranscript -out /work/bdorsalis/5.var_ann/test/snp.refGene.fa -newevf /work/bdorsalis/5.var_ann/test/snp.refGene.exonic_variant_function>

Error running system command: </share/work/biosoft/annovar/latest/table_annovar.pl /work/bdorsalis/5.var_ann/test/snp.avinput /work/bdorsalis/ref/test -buildver unknown -outfile /work/bdorsalis/5.var_ann/test/snp -remove -protocol refGene -operation g -nastring . -otherinfo>

以及在前边用sh index.sh生成unknown_refGeneMrna.fa和unknown_refGene.txt也有报错：no exons defined for group , feature gene，

当时按照提示解决的：-ignoreGroupsWithoutExons

不知道是不是这里的问题影响了后边？

这个问题我在Github上查了一下，有个人提问作者，和我的问题是一样的

作者给出的回答是手动改掉有问题的那三行，给后边加个基因名字？不知道是改哪个文件，我在snp.refGene.variant_function中没有找到有问题的那一行（synonymous SNV  gene-LOC105223489），或者直接用新的脚本覆盖掉之前的，就能解决，我尝试了 ，由于租的组学大讲堂的云服务器，没有权限，不知道我们所使用的docker镜像和云服务器中的脚本是否是最新的？

看到也有别的人提了相似的问题，可能在refGene,cytoBand,1000g2014oct_eur,1000g2014oct_afr,exac03,ljb26_all,clinvar_20140929,snp138中找不到的参考的物种蛮多的？（参考基因组是在NCBI下载的）不知道老师们能不能出一期视频讲一下如何解决这个问题，以及怎么手动修改错误的数据