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WGLab / doc-ANNOVAR

Documentation for the ANNOVAR software
http://annovar.openbioinformatics.org
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Argument "G" isn't numeric in numeric eq.... #75

Closed hamidqaedi closed 5 years ago

hamidqaedi commented 5 years ago

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?

kaichop commented 5 years ago

Read FAQ #1 and #4.

Sent from my iPhone

On Sep 21, 2019, at 10:29 AM, hamidqaedi notifications@github.com 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, line 768929. Argument "C" isn't numeric in numeric eq (==) at ./annotate_variation.pl line 2583, line 768930. Argument "A" isn't numeric in numeric eq (==) at ./annotate_variation.pl line 2583, line 768931. Argument "G" isn't numeric in numeric eq (==) at ./annotate_variation.pl line 2583, line 768932. Argument "A" isn't numeric in numeric eq (==) at ./annotate_variation.pl line 2583, line 768933. Argument "G" isn't numeric in numeric eq (==) at ./annotate_variation.pl line 2583, line 768934. Argument "G" isn't numeric in numeric eq (==) at ./annotate_variation.pl line 2583, line 768935. Argument "G" isn't numeric in numeric eq (==) at ./annotate_variation.pl line 2583, line 768936. Argument "G" isn't numeric in numeric eq (==) at ./annotate_variation.pl line 2583, line 768937. Argument "C" isn't numeric in numeric eq (==) at ./annotate_variation.pl line 2583, line 768938. Argument "C" isn't numeric in numeric eq (==) at ./annotate_variation.pl line 2583, line 768939. Argument "T" isn't numeric in numeric eq (==) at ./annotate_variation.pl line 2583, 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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hamidqaedi commented 5 years ago

Dear Dr Kai Wang, Thanks for your answer. But still I have no idea what is happening. I read both FAQs #1 and #4 . Actually FAQ #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,abraom,dbnsfp33a,ALL.sites.2015_08,clinvar_20190305,gnomad_exome,gme,kaviar_20150923 \ -operation g,f,f,f,f,f,f,f,f \ -nastring . -polish --thread 64 \ About FAQ #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

kaichop commented 5 years ago

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 notifications@github.com wrote:

Dear Dr Kai Wang, Thanks for your answer. But still I have no idea what is happening. I read both FAQs #1 https://github.com/WGLab/doc-ANNOVAR/issues/1 and #4 https://github.com/WGLab/doc-ANNOVAR/pull/4 . Actually FAQ #1 https://github.com/WGLab/doc-ANNOVAR/issues/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 https://github.com/WGLab/doc-ANNOVAR/pull/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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kaichop commented 5 years ago

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.