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WGLab / doc-ANNOVAR

Documentation for the ANNOVAR software
http://annovar.openbioinformatics.org
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-thread option slows annotation #168

Open AndreaG5 opened 3 years ago

AndreaG5 commented 3 years ago

Hi everyone!

I read about speed up annotation using -thread option but in my case seems to even slow the process.

With no option specified Annovar performs the annotation in about 30 minutes per sample (mostly due to gnomAD annotation). I decided to find a way to speed up the process and I read about -thread option. I tried with different N threads from 2 up to 16 but everytime N threads are incremented the process seems to go slower. (up to ~75 minutes per sample with -threads 10)

NOTE: Multithreading is allowed by the processor, Perl version and database folder (I checked as suggested in the documentation).

I want to know if I am doing something wrong and I am looking for solutions.

perl ./table_annovar.pl $v humandb/ -buildver hg19 -out $dir/$dir_name/$dir_name -protocol refGene,cytoBand,avsnp147,gnomad211_genome,esp6500siv2_all,clinvar_20210501,intervar_20180118,dbnsfp30a -operation gx,r,f,f,f,f,f,f -otherinfo -vcfinput -remove -xref ./humandb/gene_xref.txt -dot2underline -thread 10

System info: -OS Windows 11 Pro x64 -Intel(R) Core(TM) i9-10900F CPU @ 2.80GHz 2.81 GHz - 10 cores 20 threads