Invalid record about doc-annovar

[kaichop]

please provide details (command line etc) in FAQ #1

…

On Fri, Jun 9, 2023 at 6:01 AM syuxuan ***@***.***> wrote: Hi, I am trying to do region annotation, and the error message is that NOTICE: Reading annotation database humandb/hg19_phastConsElements100way.txt ... Error: invalid record in dbfile humandb/hg19_phastConsElements100way.txt (6 fields expected): <585 chr1 10917 11941 chr1.0 1 1024 0 /gbdb/hg19/multiz100way/phastCons100way.wib 0 0.522 1024 49.403 9.82319> Is this problem due to the dbfile or my own input file? I have tried 46ways, it also gives me similer error message as follows: NOTICE: Reading annotation database humandb/hg19_phastConsElements46way.txt ... Error: invalid record in dbfile humandb/hg19_phastConsElements46way.txt (6 fields expected): <896 chr19 40834360 40> Thanks for your help! — Reply to this email directly, view it on GitHub <#223>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNG3OC4OGMRUSCJKPBZUCTXKLX6JANCNFSM6AAAAAAZANUAUY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[syuxuan]

The command line is
annotate_variation.pl -regionanno -build hg19 -out D_annov -dbtype phastConsElements100way /data/work/D_annov.txt humandb/

The input file is attached and part of my input
D_annov.txt
file is the following
1 751343 751343 A T rs28544273
1 751756 751756 C T rs143225517
1 752566 752566 G A rs3094315
1 753405 753405 C A rs61770173
1 768253 768253 A C rs2977608

The Error message in screen is

NOTICE: Output file is written to AD_annovar_part.hg19_phastConsElements100way

NOTICE: Reading annotation database humandb/hg19_phastConsElements100way.txt ... Error: invalid record in dbfile humandb/hg19_phastConsElements100way.txt (6 fields expected): <585 chr1 10917 11941 chr1.0 1 1024 0 /gbdb/hg19/multiz100way/phastCons100way.wib 0 0.522 1024 49.403 9.82319>

The output file shows that

ANNOVAR Version:
$Date: 2020-06-07 23:56:37 -0400 (Sun, 7 Jun 2020) $
ANNOVAR Information:
For questions, comments, documentation, bug reports and program update, please visit http://www.openbioinformatics.org/annovar/
ANNOVAR Command:
annotate_variation.pl -regionanno -build hg19 -out D_annov -dbtype phastConsElements100way /data/D_annov.txt humandb/
ANNOVAR Started:
Tue Jun 13 18:15:42 2023
NOTICE: Output file is written to D_annov.hg19_phastConsElements100way
NOTICE: Reading annotation database humandb/hg19_phastConsElements100way.txt ...

Thanks!

[syuxuan]

Thanks for the guidance! I redownload the latest reference file and it works!