Argument "G" isn't numeric in numeric eq.... #75
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On Sep 21, 2019, at 10:29 AM, hamidqaedi ***@***.***> wrote:
Hi Developers,
Just before finishing the command "table_annovar.pl" , lines are printing on the screen.
`Argument "G" isn't numeric in numeric eq (==) at ./annotate_variation.pl line 2583, <DB> line 768929.
Argument "C" isn't numeric in numeric eq (==) at ./annotate_variation.pl line 2583, <DB> line 768930.
Argument "A" isn't numeric in numeric eq (==) at ./annotate_variation.pl line 2583, <DB> line 768931.
Argument "G" isn't numeric in numeric eq (==) at ./annotate_variation.pl line 2583, <DB> line 768932.
Argument "A" isn't numeric in numeric eq (==) at ./annotate_variation.pl line 2583, <DB> line 768933.
Argument "G" isn't numeric in numeric eq (==) at ./annotate_variation.pl line 2583, <DB> line 768934.
Argument "G" isn't numeric in numeric eq (==) at ./annotate_variation.pl line 2583, <DB> line 768935.
Argument "G" isn't numeric in numeric eq (==) at ./annotate_variation.pl line 2583, <DB> line 768936.
Argument "G" isn't numeric in numeric eq (==) at ./annotate_variation.pl line 2583, <DB> line 768937.
Argument "C" isn't numeric in numeric eq (==) at ./annotate_variation.pl line 2583, <DB> line 768938.
Argument "C" isn't numeric in numeric eq (==) at ./annotate_variation.pl line 2583, <DB> line 768939.
Argument "T" isn't numeric in numeric eq (==) at ./annotate_variation.pl line 2583, <DB> line 768940.
Done
`
This is while all the process for me take about 20 minutes to complete just before the step of printing the lines. The printing takes about 1 hour. Just after this process is done, I receive comments show the annotation job is done.
Any suggestion?
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Dear Dr Kai Wang, |
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FAQ #1 asked you to send the actual command so that I can advise what is
wrong.
FAQ #4 gives the keyword to use. In this case, ALL.sites.2015_08 is not the
correct keyword to use, and you have to use 1000g2015aug_all instead due to
historical reasons. I may change the program to handle the keyword issue
because it is a re-occurring issue for many people.
…On Sun, Oct 13, 2019 at 11:30 AM hamidqaedi ***@***.***> wrote:
Dear Dr Kai Wang,
Thanks for your answer.
But still I have no idea what is happening. I read both FAQs #1
<#1> and #4
<#4> .
Actually FAQ #1 <#1> is about
using -vcfinput and -csvout in the command. This is not my case.
I am using annovar as a part of my pipeline and the code chunk relevant to
annovar in my script is as follows:
rule avinput: input: "VCF_final/{sample}_filtered_final.vcf", output:
"ANNO/avi.{sample}.avinput", params: toanno = CTA, priority:14, shell: """
mkdir -p ANNO perl {params.toanno} -format vcf4 {input} -outfile ./ANNO/avi
-allsample -include -withzyg > {output} """ rule annovar: input:
rules.avinput.output, output: "ANNO/{sample}.hg19_multianno.txt", params:
table2annovar = TTA, humandb = HUMANDB, priority:15, shell: """ perl
{params.table2annovar} {input} {params.humandb} \ -buildver hg19 -out
/ANNO/sample\ -remove \ -protocol
refGene,avsnp150,iranome,abraom,dbnsfp33a,ALL.sites.2015_08,clinvar_20190305,gnomad_exome,gme,kaviar_20150923
\ -operation g,f,f,f,f,f,f,f,f,f \ -nastring . -polish --thread 64 \
About FAQ #4 <#4> I am not sure
what to do. Do I need to change default of an annovar config file ?
Appreciate your time and reply.
Hamid
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This is a re-occurring issue and I have made changes to code so that ALL.sites.2015_08 can be a valid keyword in future versions of ANNOVAR. It will be released soon. I will close this issue. |
Hi Developers,
Just before finishing the command "table_annovar.pl" , lines are printing on the screen.
This is while all the process for me take about 20 minutes to complete just before the step of printing the lines. The printing takes about 1 hour. Just after this process is done, I receive comments show the annotation job is done.
Any suggestion?
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