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line 1:11 no viable alternative at input '[*].GENE:' #53

Closed AroobAlhumaidy closed 3 years ago

AroobAlhumaidy commented 3 years ago

Hello, i followed the instructions on this page https://pcingola.github.io/SnpEff/ss_extractfields/ in order to use extractfields to separate annotations in separate columns.. I used this command:

$ cat my.ann1.vcf | /mnt/e/Bioinformatics/tools/snpeff/snpEff/scripts/vcfEffOnePerLine.pl | java -jar /mnt/e/Bioinformatics/tools/snpeff/snpEff/SnpSift.jar extractFields - CHROM POS REF ALT QUAL DP ANN "ANN[].ALLELE" "ANN[].EFFECT" "ANN[].IMPACT:" "ANN[].GENE:" "ANN[].GENEID:" ANN[].FEATURE" "ANN[].FEATUREID" "ANN[].BIOTYPE:" "ANN[].RANK:" "ANN[].HGVS_C" "ANN[].HGVS_P" "ANN[].CDNA_POS" "ANN[].CDNA_LEN" "ANN[].CDS_POS" "ANN[].CDS_LEN" "ANN[].AA_POS" "ANN[].AA_LEN" "ANN[].DISTANCE" "ANN[*].ERRORS" > snpsiftout8.vcf \

I faced 2 issues: 1- the code hanged at > sign, for longer time than expected 2- I tried to shorten the parameters in order to see where is the hang, by using: $ cat my.ann.vcf | /mnt/e/Bioinformatics/tools/snpeff/snpEff/scripts/vcfEffOnePerLine.pl |java -jar /mnt/e/Bioinformatics/tools/snpeff/snpEff/SnpSift.jar extractFields - CHROM POS REF ALT QUAL DP "ANN[].ALLELE" "ANN[].EFFECT" "ANN[].GENE:" "ANN[].GENEID:" > snpsiftout2.vcf

then I got: line 1:11 no viable alternative at input '[].GENE:' line 1:13 no viable alternative at input '[].GENEID:'

I appreciate any insights,

Thanks Capture1

aknfa commented 3 years ago

Did you fix your problem? I encountered the same output.

aknfa commented 3 years ago

I found what was an issue. You need to remove colons (:) from the script. So it should turn to "ANN[].IMPACT" from "ANN[].IMPACT:"

AroobAlhumaidy commented 3 years ago

yes it's solved, i used this command:

$ cat my.ann.vcf | /e/Bioinformatics/tools/snpeff/scripts/vcfEffOnePerLine.pl | java -jar /e/Bioinformatics/tools/snpeff/SnpSift.jar extractFields - CHROM POS ID REF ALT QUAL DP FILTER "ANN[].ALLELE" "ANN[].GENE" "ANN[].EFFECT" "ANN[].HGVS_P" "ANN[].FEATURE" "ANN[].FEATUREID" "ANN[].HGVS_C" "ANN[].CDNA_POS" "ANN[].CDNA_LEN" "ANN[].CDS_POS" "ANN[].CDS_LEN" "ANN[].AA_POS" "ANN[].AA_LEN" "ANN[].DISTANCE" "ANN[].ERRORS" "ANN[].GENEID" "ANN[].BIOTYPE" "ANN[].RANK" > snpsiftout.vcf