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WGLab / doc-ANNOVAR

Documentation for the ANNOVAR software
http://annovar.openbioinformatics.org
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Error running system commands #215

Closed surakshavinod closed 1 year ago

surakshavinod commented 1 year ago

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 1 year ago

What is the actual command and the actual error message?

On Tue, Mar 7, 2023 at 11:46 PM Suraksha Vinod @.***> wrote:

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 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

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surakshavinod commented 1 year ago

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 1 year ago

If your file is huge (like 10 million variants, or thousands of samples), then it is possible that there is a out of memory error. Since you masked the numbers below it is hard to tell. However, you could just run the system command yourself and see output (perhaps this gives some clue). This command seems to be the one that leads to error message.

annotate_variation.pl -geneanno -buildver hg38 -dbtype refGene -outfile myanno.refGene -exonsort -nofirstcodondel myanno.avinput humandb

On Wed, Mar 8, 2023 at 12:38 AM Suraksha Vinod @.***> wrote:

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

This the 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

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surakshavinod commented 1 year ago

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 1 year ago

Thank you for letting me know.

On Fri, Mar 24, 2023 at 8:19 AM Suraksha Vinod @.***> wrote:

Hi @kaichop https://github.com/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!

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