reseqv2.0镜像annovar报错
在使用annovar对vcf进行注释的时候出现报错错误信息如下
[root@8fbb0720ada0 09:47:30 /work/my_reseq/5.var_ann]# table_annovar.pl $workdir/4.snp_indel/var_qc/pyb4.clean.vcf.gz $refdir -buildver unknown -out $workdir/5.var_ann/snp -remove -protocol refGene -operation g -nastring . -vcfinput
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/my_reseq/4.snp_indel/var_qc/pyb4.clean.vcf.gz > /work/my_reseq/5.var_ann/snp.avinput>
NOTICE: Finished reading 656047 lines from VCF file
NOTICE: A total of 656008 locus in VCF file passed QC threshold, representing 541319 SNPs (375593 transitions and 165726 transversions) and 114689 indels/substitutions
NOTICE: Finished writing allele frequencies based on 1082638 SNP genotypes (751186 transitions and 331452 transversions) and 229378 indels/substitutions for 2 samples
NOTICE: Running with system command </share/work/biosoft/annovar/latest/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>
NOTICE: the --polish argument is set ON automatically (use --nopolish to change this behavior)
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NOTICE: Processing operation=g protocol=refGene
NOTICE: Running with system command <annotate_variation.pl -geneanno --neargene 1000 -buildver unknown -dbtype refGene -outfile /work/my_reseq/5.var_ann/snp.refGene -exonsort -nofirstcodondel /work/my_reseq/5.var_ann/snp.avinput /work/my_reseq/ref>
NOTICE: Output files are 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 66338 transcripts (including 0 without coding sequence annotation) for 55986 unique genes
NOTICE: Processing next batch with 656008 unique variants in 656008 input lines
NOTICE: Reading FASTA sequences from /work/my_reseq/ref/unknown_refGeneMrna.fa ... Done with 14055 sequences
WARNING: A total of 6 sequences will be ignored due to lack of correct ORF annotation
WARNING: invalid triplets found in DNA sequence to be translated: <NCN>
Use of uninitialized value in concatenation (.) or string at /share/work/biosoft/annovar/latest/annotate_variation.pl line 3293.
WARNING: invalid triplets found in DNA sequence to be translated: <CGN>
Use of uninitialized value in concatenation (.) or string at /share/work/biosoft/annovar/latest/annotate_variation.pl line 3293.
WARNING: invalid triplets found in DNA sequence to be translated: <TNC>
Use of uninitialized value in concatenation (.) or string at /share/work/biosoft/annovar/latest/annotate_variation.pl line 3293.
WARNING: invalid triplets found in DNA sequence to be translated: <GNC>
Use of uninitialized value in concatenation (.) or string at /share/work/biosoft/annovar/latest/annotate_variation.pl line 3293.
WARNING: invalid triplets found in DNA sequence to be translated: <NGC>
Use of uninitialized value in concatenation (.) or string at /share/work/biosoft/annovar/latest/annotate_variation.pl line 3293.
WARNING: invalid triplets found in DNA sequence to be translated: <NGG>
Use of uninitialized value in concatenation (.) or string at /share/work/biosoft/annovar/latest/annotate_variation.pl line 3293.
WARNING: invalid triplets found in DNA sequence to be translated: <GNA>
Use of uninitialized value in concatenation (.) or string at /share/work/biosoft/annovar/latest/annotate_variation.pl line 3293.
WARNING: invalid triplets found in DNA sequence to be translated: <CGN>
Use of uninitialized value in concatenation (.) or string at /share/work/biosoft/annovar/latest/annotate_variation.pl line 3293.
WARNING: invalid triplets found in DNA sequence to be translated: <TCN>
Use of uninitialized value in concatenation (.) or string at /share/work/biosoft/annovar/latest/annotate_variation.pl line 3293.
WARNING: invalid triplets found in DNA sequence to be translated: <CGN>
Use of uninitialized value in concatenation (.) or string at /share/work/biosoft/annovar/latest/annotate_variation.pl line 3293.
NOTICE: Running with system command <coding_change.pl /work/my_reseq/5.var_ann/snp.refGene.exonic_variant_function.orig /work/my_reseq/ref/unknown_refGene.txt /work/my_reseq/ref/unknown_refGeneMrna.fa -alltranscript -out /work/my_reseq/5.var_ann/snp.refGene.fa -newevf /work/my_reseq/5.var_ann/snp.refGene.exonic_variant_function>
Died at /share/work/biosoft/annovar/latest/coding_change.pl line 677.
Error running system command: <coding_change.pl /work/my_reseq/5.var_ann/snp.refGene.exonic_variant_function.orig /work/my_reseq/ref/unknown_refGene.txt /work/my_reseq/ref/unknown_refGeneMrna.fa -alltranscript -out /work/my_reseq/5.var_ann/snp.refGene.fa -newevf /work/my_reseq/5.var_ann/snp.refGene.exonic_variant_function>
Error running system command: </share/work/biosoft/annovar/latest/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>
最后生成的文件缺少snp.unknown_multianno.vcf和snp.unknown_multianno.txt
请各位老师帮忙看看如何解决 感谢
最后生成的文件缺少snp.unknown_multianno.vcf和snp.unknown_multianno.txt
请各位老师帮忙看看如何解决 感谢