InterVar always downloads 1000g2015aug. Says it is not in the provided directory.

[ryhamz]

For now, I have just removed Intervar's check for the file and subsequent call to Annovar's Perl script. Perhaps you or I could review this section of Intervar code at some point.

Notice: Your command of InterVar is ['/home/tools/InterVar/Intervar.py', '-c', 'config.ini', '--table_annovar=/home/tools/annovar/table_annovar.pl', '--convert2annovar=/home/tools/annovar/convert2annovar.pl', '--annotate_variation=/home/tools/annovar/annotate_variation.pl', '--database_locat=/home/tools/annovar/humandb', '--input_type=VCF', '--input=/home/ngs-projects/ThuPerfTest/vcf/ThuPerfTest.35genes_woIntron.QCed.SplitMultiAllelic.vcf', '--output=/home/ngsprojects/ThuPerfTest/vcf/intervar/ThuPerfTest.35genes_woIntron.QCed.SplitMultiAllelic']

INFO: The options are {'pp2_genes': 'intervardb/PP2.genes', 'inputfile': '/home/ngs-projects/ThuPerfTest/vcf/ThuPerfTest.35genes_woIntron.QCed.SplitMultiAllelic.vcf', 'exclude_snps': 'interv
ardb/ext.variants.hg19', 'annotate_variation': '/home/tools/annovar/annotate_variation.pl', 'ps4_snps': 'intervardb/PS4.variants.hg19', 'mim_recessive': 'intervardb/mim_recessive.txt', 'curr
ent_version': 'Intervar_20151116', 'bs2_snps': 'intervardb/BS2_hom_het.hg19', 'evidence_file': 'None', 'public_dev': 'https://github.com/WGLab/InterVar/releases', 'otherinfo': 'FALSE', 'data
base_names': 'refGene esp6500siv2_all 1000g2015aug avsnp144 dbnsfp30a clinvar_20160302 exac03 dbscsnv11 dbnsfp31a_interpro rmsk ensGene knownGene', 'mim_pheno': 'intervardb/mim_pheno.txt', '
table_annovar': '/home/tools/annovar/table_annovar.pl', 'buildver': 'hg19', 'inputfile_type': 'VCF', 'onetranscript': 'FALSE', 'mim2gene': 'intervardb/mim2gene.txt', 'orpha': 'intervardb/orp
ha.txt', 'ps1_aa': 'intervardb/PS1.AA.change.patho.hg19', 'mim_adultonset': 'intervardb/mim_adultonset.txt', 'morbidmap': 'intervardb/morbidmap', 'outfile': '/home/ngs-projects/ThuPerfTest/v
cf/intervar/ThuPerfTest.35genes_woIntron.QCed.SplitMultiAllelic', 'csvout': 'FALSE', 'knowngenecanonical': 'intervardb/knownGeneCanonical.txt', 'dot2underline': 'TRUE', 'convert2annovar': '/
home/tools/annovar/convert2annovar.pl', 'database_locat': '/home/tools/annovar/humandb', 'database_intervar': 'intervardb', 'lof_genes': 'intervardb/PVS1.LOF.genes', 'disorder_cutoff': '0.01
', 'mim_domin': 'intervardb/mim_domin.txt', 'pm1_domain': 'intervardb/PM1_domains_with_benigns', 'mim_orpha': 'intervardb/mim_orpha.txt', 'bp1_genes': 'intervardb/BP1.genes'} 

Warning: the folder of /home/tools/annovar/humandb is already created!

Warning: The Annovar dataset file of 1000g2015aug is not in /home/tools/annovar/humandb,begin to download this /home/tools/annovar/humandb/hg19_1000g2015aug.txt ...
perl /home/tools/annovar/annotate_variation.pl -buildver hg19 -downdb -webfrom annovar 1000g2015aug /home/tools/annovar/humandb

My humandb directory contains these files:

GRCh37_MT_ensGeneMrna.fa        hg19_AMR.sites.2015_08.txt.idx  hg19_SAS.sites.2015_08.txt.idx  hg19_dbnsfp31a_interpro.txt.idx  hg19_exac03.txt.idx          hg19_refGeneVersion.txt
annovar_downdb.log              hg19_EAS.sites.2015_08.txt      hg19_avsnp144.txt               hg19_dbscsnv11.txt               hg19_example_db_generic.txt  hg19_rmsk.txt
genometrax-sample-files-gff     hg19_EAS.sites.2015_08.txt.idx  hg19_avsnp144.txt.idx           hg19_dbscsnv11.txt.idx           hg19_example_db_gff3.txt
hg19_AFR.sites.2015_08.txt      hg19_EUR.sites.2015_08.txt      hg19_clinvar_20160302.txt       hg19_ensGene.txt                 hg19_kgXref.txt
hg19_AFR.sites.2015_08.txt.idx  hg19_EUR.sites.2015_08.txt.idx  hg19_clinvar_20160302.txt.idx   hg19_ensGeneMrna.fa              hg19_knownGene.txt
hg19_ALL.sites.2015_08.txt      hg19_MT_ensGene.txt             hg19_dbnsfp30a.txt              hg19_esp6500siv2_all.txt         hg19_knownGeneMrna.fa
hg19_ALL.sites.2015_08.txt.idx  hg19_MT_ensGeneMrna.fa          hg19_dbnsfp30a.txt.idx          hg19_esp6500siv2_all.txt.idx     hg19_refGene.txt```

[quanliustc]

please update the intervar, your version of 'Intervar_20151116' is outdated.

[ryhamz]

@quanliustc

I updated and that resolves it.

Is there a way to auto-update?