Failure in Annonatation with Annovar

Question

[Can Abdullah]

I am trying to perform an annotation with table_annovar.pl script, to annotate my variants in my .avinput file but It seems that the annotate_variation.pl script is being called within the table_annovar.pl script, and there is an error with the command being executed.

Here is my command and the error message I got:

/home/cancam/Desktop/THESIS\ PROJECT/annovar/table_annovar.pl -buildver hg38 -protocol gnomad211_genome,clinvar_20221231,dbnsfp42a,refGene -operation f,f,f,g -nastring . -otherinfo -csvout -out "/home/cancam/Desktop/THESIS PROJECT/justone/outputs/UniPD_0003" "/home/cancam/Desktop/THESIS PROJECT/justone/UniPD_0003.avinput" "/home/cancam/Desktop/THESIS PROJECT/annovar/humandb/"

Syntax error
Usage:
     annotate_variation.pl [arguments] <query-file|table-name> <database-location>

Error running system command: <annotate_variation.pl -filter -dbtype gnomad211_genome -buildver hg38 -outfile /home/cancam/Desktop/THESIS PROJECT/justone/outputs/UniPD_0003 /home/cancam/Desktop/THESIS PROJECT/justone/UniPD_0003.avinput /home/cancam/Desktop/THESIS PROJECT/annovar/humandb/ -otherinfo>