WGLab/doc-ANNOVAR

Error running system commands

surakshavinod opened this issue · 5 comments

surakshavinod commented

Hi, I'm using Annovar to annotate my VCF file and I'm running into an error. Please find below the command and the errors:

Command:
perl table_annovar.pl <input.recode.vcf> humandb/ -buildver hg38 -out myanno -remove -protocol refGene,cytoBand,dbnsfp30a -operation g,r,f -nastring . -vcfinput

Errors:

Error running system command: <annotate_variation.pl -geneanno -buildver hg38 -dbtype refGene -outfile myanno.refGene -exonsort -nofirstcodondel myanno.avinput humandb/>
Error running system command: <table_annovar.pl myanno.avinput humandb/ -buildver hg38 -outfile myanno -remove -protocol refGene,cytoBand,dbnsfp30a -operation g,r,f -nastring . -otherinfo>

Thanks,
Suraksha

kaichop commented
surakshavinod commented

Hi @kaichop, thank you for your quick reply! Please find below the actual command used and the error log:

Command used:
perl table_annovar.pl input.recode.vcf humandb/ -buildver hg38 -out myanno -remove -protocol refGene,cytoBand,dbnsfp30a -operation g,r,f -nastring . -vcfinput

Error log (Please note I have replaced the actual numbers with <>):

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 input.recode.vcf > myanno.avinput>
NOTICE: Finished reading <> lines from VCF file
NOTICE: A total of <> locus in VCF file passed QC threshold, representing <> SNPs (<> transitions and <> transversions) and <> indels/substitutions
NOTICE: Finished writing allele frequencies based on <> SNP genotypes (<> transitions and <> transversions) and <> indels/substitutions for <> samples
NOTICE: Running with system command <table_annovar.pl myanno.avinput humandb/ -buildver hg38 -outfile myanno -remove -protocol refGene,cytoBand,dbnsfp30a -operation g,r,f -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 -buildver hg38 -dbtype refGene -outfile myanno.refGene -exonsort -nofirstcodondel myanno.avinput humandb/>
NOTICE: Output files are written to myanno.refGene.variant_function, myanno.refGene.exonic_variant_function
NOTICE: Reading gene annotation from humandb/hg38_refGene.txt ... Done with <> transcripts (including <> without coding sequence annotation) for <> unique genes
Error running system command: <annotate_variation.pl -geneanno -buildver hg38 -dbtype refGene -outfile myanno.refGene -exonsort -nofirstcodondel myanno.avinput humandb/>
Error running system command: <table_annovar.pl myanno.avinput humandb/ -buildver hg38 -outfile myanno -remove -protocol refGene,cytoBand,dbnsfp30a -operation g,r,f -nastring . -otherinfo>

Could there be something wrong with the VCF file format itself?

Thanks,
Suraksha

kaichop commented
surakshavinod commented

Hi @kaichop ,

My sincere apologies for the late reply. If we break the file in chunks and run it, the command works perfectly fine, so as you mentioned, I believe it's an out-of-memory error.

Thank you so much for your help!

kaichop commented
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