$ grep -E "(ERR|WARN)" *.err
_Pindel_Patient157t10.err:WARNING: Your index file /home/shared/cbc/software_cbc/annovar-2011-10-02/hg19db/hg19_ALL.sites.2010_11.txt.idx is out of date and will not be used. ANNOVAR can still generate correct results without index file.
_Pindel_Patient157t10.err:WARNING: Unable to load database index successfully from file /home/shared/cbc/software_cbc/annovar-2011-10-02/hg19db/hg19_ALL.sites.2010_11.txt.idx.
From the message this is just a warning. I guess, ANNOVAR will generate the index file on the fly, which probably introduces unnecessary overhead. The files involved are:
$ ll /home/shared/cbc/software_cbc/annovar-2011-10-02/hg19db/
total 12595908
drwxr-xr-x 2 henrik cbc 4096 Oct 1 2020 .
drwxr-xr-x 5 henrik cbc 331 Mar 19 2018 ..
-rwxr-xr-x 1 henrik cbc 4521 Aug 9 2012 annovar_downdb.log
-rw-r--r-- 1 henrik cbc 677701547 Oct 4 2011 hg19_ALL.sites.2010_11.txt
-rw-r--r-- 1 henrik cbc 87287220 Feb 22 2012 hg19_ALL.sites.2010_11.txt.idx
-rwxr-xr-x 1 henrik cbc 890172775 Oct 31 2011 hg19_ALL.sites.2011_05.txt
-rwxr-xr-x 1 henrik cbc 895119 Oct 31 2011 hg19_ALL.sites.2011_05.txt.idx
-rwxr-xr-x 1 henrik cbc 2609192331 Sep 12 2011 hg19_avsift.txt
-rwxr-xr-x 1 henrik cbc 6317127 Feb 22 2012 hg19_avsift.txt.idx
-rwxr-xr-x 1 henrik cbc 122040253 Oct 31 2011 hg19_refGeneMrna.fa
-rwxr-xr-x 1 henrik cbc 11463062 Oct 31 2011 hg19_refGene.txt
-rwxr-xr-x 1 henrik cbc 26764953 Oct 31 2011 hg19_refLink.txt
-rw-r-xr-- 1 henrik cbc 2047365487 Dec 6 2011 hg19_snp130.txt
-rwxr-xr-x 1 henrik cbc 6418015148 Oct 31 2011 hg19_snp132.txt
-rwxr-xr-x 1 henrik cbc 958385 Oct 31 2011 hg19_snp132.txt.idx
From the message this is just a warning. I guess, ANNOVAR will generate the index file on the fly, which probably introduces unnecessary overhead. The files involved are: