注释SNP一直报错 ,并未提报错原因，生成的文件snp.avinput有数据，snp.refGene.invalid inputsnp.refGene.logsnp,refGene.variant functionsnp,refGene,exonic variant这几个大小为0，运行提示如下NOTICE: Running with system command <convert2annovar.pl -includeinfo -allsample -withfreq -format vcf4 /work/my_reseq/4.snp_indel/all.clean.snp.vcf.gz > /work/my_reseq/5.var_ann/snp.avinput>
NOTICE: Finished reading 5099177 lines from VCF file
NOTICE: A total of 5099109 locus in VCF file passed QC threshold, representing 5099109 SNPs (3715827 transitions and 1383282 transversions) and 0 indels/substitutions
NOTICE: Finished writing allele frequencies based on 2365986576 SNP genotypes (1724143728 transitions and 641842848 transversions) and 0 indels/substitutions for 464 samples
NOTICE: Running with system command </biosoft/annovar/2018Apr16/table_annovar.pl /work/my_reseq/5.var_ann/snp.avinput /work/my_reseq/ref -buildver unknown -outfile /work/my_reseq/5.var_ann/snp -remove -protocol refGene -operation g -nastring . -otherinfo>
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NOTICE: Processing operation=g protocol=refGene
NOTICE: Running with system command <annotate_variation.pl -geneanno -buildver unknown -dbtype refGene -outfile /work/my_reseq/5.var_ann/snp.refGene -exonsort /work/my_reseq/5.var_ann/snp.avinput /work/my_reseq/ref>
NOTICE: Output files were written to /work/my_reseq/5.var_ann/snp.refGene.variant_function, /work/my_reseq/5.var_ann/snp.refGene.exonic_variant_function
NOTICE: Reading gene annotation from /work/my_reseq/ref/unknown_refGene.txt ... Done with 56553 transcripts (including 0 without coding sequence annotation) for 56553 unique genes
Error running system command: <annotate_variation.pl -geneanno -buildver unknown -dbtype refGene -outfile /work/my_reseq/5.var_ann/snp.refGene -exonsort /work/my_reseq/5.var_ann/snp.avinput /work/my_reseq/ref>
Error running system command: </biosoft/annovar/2018Apr16/table_annovar.pl /work/my_reseq/5.var_ann/snp.avinput /work/my_reseq/ref -buildver unknown -outfile /work/my_reseq/5.var_ann/snp -remove -protocol refGene -operation g -nastring . -otherinfo>，请老师解答
