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WGLab / InterVar

A bioinformatics software tool for clinical interpretation of genetic variants by the 2015 ACMG-AMP guideline
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dear lee, where can I download “the annotation result file from ANNOVAR”？the last two sentences of ERROR #19

Closed pkphcwj closed 6 years ago

pkphcwj commented 6 years ago

img_0877 wdeMacBook:InterVar-1.0.8 wj$ python Intervar.py -i example/ex1.avinput -o example/myanno --evidence_file=evdience.txt

InterVar
Interpretation of Pathogenic/Benign for variants using python scripts of InterVar.

%prog 0.1.7 20170608 Written by Quan LI,leequan@gmail.com. InterVar is free for non-commercial use without warranty. Please contact the authors for commercial use. Copyright (C) 2016 Wang Genomic Lab

Notice: Your command of InterVar is ['Intervar.py', '-i', 'example/ex1.avinput', '-o', 'example/myanno', '--evidence_file=evdience.txt'] Warning: You provided your own evidence file [ evdience.txt ] for the InterVar. Warning: Your specified evidence file [ evdience.txt ] is not here,please check the path of your evidence file. Your analysis will begin without your specified evidence. INFO: The options are {'pp2_genes': 'intervardb/PP2.genes', 'inputfile': 'example/ex1.avinput', 'exclude_snps': 'intervardb/ext.variants.hg19', 'annotate_variation': './annotate_variation.pl', 'ps4_snps': 'intervardb/PS4.variants.hg19', 'mim_domin': 'intervardb/mim_domin.txt', 'current_version': 'Intervar_20170228', 'bs2_snps': 'intervardb/BS2_hom_het.hg19', 'evidence_file': 'evdience.txt', 'public_dev': 'https://github.com/WGLab/InterVar/releases', 'otherinfo': 'TRUE', 'database_names': 'refGene esp6500siv2_all 1000g201508 avsnp144 dbnsfp30a clinvar_20160302 exac03 dbscsnv11 dbnsfp31a_interpro rmsk ensGene knownGene', 'mim_pheno': 'intervardb/mim_pheno.txt', 'table_annovar': './table_annovar.pl', 'buildver': 'hg19', 'inputfile_type': 'AVinput', 'onetranscript': 'FALSE', 'mim2gene': 'intervardb/mim2gene.txt', 'orpha': 'intervardb/orpha.txt', 'ps1_aa': 'intervardb/PS1.AA.change.patho.hg19', 'mim_adultonset': 'intervardb/mim_adultonset.txt', 'knowngenecanonical': 'intervardb/knownGeneCanonical.txt', 'outfile': 'example/myanno', 'convert2annovar': './convert2annovar.pl', 'database_locat': 'humandb', 'database_intervar': 'intervardb', 'lof_genes': 'intervardb/PVS1.LOF.genes', 'disorder_cutoff': '0.01', 'mim_recessive': 'intervardb/mim_recessive.txt', 'pm1_domain': 'intervardb/PM1_domains_with_benigns', 'mim_orpha': 'intervardb/mim_orpha.txt', 'bp1_genes': 'intervardb/BP1.genes'} Warning: the folder of humandb is already created! Warning: The Annovar dataset file of 1000g201508 is not in humandb,begin to download this humandb/hg19_1000g201508.txt ... perl ./annotate_variation.pl -buildver hg19 -downdb -webfrom annovar 1000g201508 humandb NOTICE: Web-based checking to see whether ANNOVAR new version is available ... Done NOTICE: Downloading annotation database http://www.openbioinformatics.org/annovar/download/hg19_1000g201508.txt.gz ... Failed NOTICE: Downloading annotation database http://www.openbioinformatics.org/annovar/download/hg19_1000g201508.txt.idx.gz ... Failed WARNING: Some files cannot be downloaded, including http://www.openbioinformatics.org/annovar/download/hg19_1000g201508.txt.gz, http://www.openbioinformatics.org/annovar/download/hg19_1000g201508.txt.idx.gz perl ./table_annovar.pl example/ex1.avinput humandb -buildver hg19 -remove -out example/myanno -protocol refGene,esp6500siv2_all,1000g2015aug_all,avsnp144,dbnsfp30a,clinvar_20160302,exac03,dbscsnv11,dbnsfp31a_interpro,rmsk,ensGene,knownGene -operation g,f,f,f,f,f,f,f,f,r,g,g -nastring . --otherinfo Error: the required database file humandb/hg19_ALL.sites.201508.txt does not exist. Warning: The InterVar seems not run correctly, please check your inputs , options and configure file! **ERROR: The InterVar did not find the annotation result file from ANNOVAR!_* ERROR: The name of annotation result file should be like example/myanno.hg19__multianno.txt

Thanks for using InterVar! Report bugs to leequan@gmail.com; InterVar homepage: http://wInterVar.wglab.org

quanliustc commented 6 years ago

what's your annovar version? It seems the annovar annotation dataset of 1000g2015aug has not been downloaded.

pkphcwj commented 6 years ago

I find the latest intervar doesn't have the following two: inflating: InterVar-master/example/myanno.hg19_multianno.txt inflating: InterVar-master/example/myanno.hg19_multianno.txt.grl_p

kaichop commented 6 years ago

@pkphcwj you should NEVER share a URL that is protected to public sites. This is absolutely not allowed.

kaichop commented 6 years ago

InterVar is available at GitHub that you can download, but ANNOVAR requires a specific registration process. This is different.

pkphcwj commented 6 years ago

ok...I am so so so ...sorry for my fault!I will never do it again.i really need ur help for the use of intervar.

pkphcwj commented 6 years ago

I have redownlaoded the intervar and annovar ，but the myanno.hg19_multianno.txt and annovar annotation dataset of 1000g2015aug still doesn't exist. whats wrong with it?

quanliustc commented 6 years ago

myanno.hg19_multianno.txt is the example output of Annovar, Make sure your ANNOVAR is updated and also intervar updated , if the ANNOVAR and intervar are all new, then you should see :

NOTICE: Downloading annotation database http://www.openbioinformatics.org/annovar/download/hg19_1000g2015aug.zip

not download the hg19_1000g201508.txt.gz

quanliustc commented 6 years ago

also update the config,ini file from github, and I can see your config,ini file also are outdated.

pkphcwj commented 6 years ago

@quanliustc THANK U SO MUCH! it works now,i added hg19_1000g201508aug in the humandb of intervar and went on!