Invalid record

[syuxuan]

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!

[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!

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[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!