snpEff and GATK errors; "Try installing the appropriate database."

[Ivan De Dios]

Hi Brad,

Recently I upgraded bcbio-nextgen on a system which had not received updates in over 1 year.

The error message is as follows:

java.lang.RuntimeException: Database file '/usr/local/share/bcbio/genomes/Hsapiens/GRCh37/snpeff/GRCh37.75/snpEffectPredictor.bin' is not compatible with this program version:
    Database version : '4.2'
    Program version : '4.3'
Try installing the appropriate database.

Currently I'm getting this error and another one pertaining to GATK and malformed headers in the input vcfs

Htsjdk.tribble.TribbleException$MalformedFeatureFile: Unable to parse header with error: Your input file has a malformed header: We never saw the required CHROM header line (starting with one #) for the input VCF file, for input source: /isilon/scratch/NS-081016/work/mutect2/1/NTP16-003495M-1_0_36932509.vcf.gz

Would doing a clean install be the quickest fix for this or are there settings I need to change that can resolve these.

Thanks,
Ivan De Dios

[Brad Chapman]

Ivan;
Sorry about the upgrade issues. You shouldn't need a clean installation and an
additional update should fix it.

> The error message is as follows:
> java.lang.RuntimeException: Database file
> '/usr/local/share/bcbio/genomes/Hsapiens/GRCh37/snpeff/GRCh37.75/snpEffectPredictor.bin'
> is not compatible with this program version:
> Database version : '4.2'
> Program version : '4.3'
> Try installing the appropriate database.

You should also include the data target to the upgrade:

bcbio_nextgen.py upgrade --data

so it'll update the snpEff databases to the latest version.

> Currently I'm getting this error and another one pertaining to GATK and
> malformed headers in the input vcfs
>
> Htsjdk.tribble.TribbleException$MalformedFeatureFile: Unable to parse
> header with error: Your input file has a malformed header: We never saw the
> required CHROM header line (starting with one #) for the input VCF file,
> for input source:
> /isilon/scratch/NS-081016/work/mutect2/1/NTP16-003495M-1_0_36932509.vcf.gz

What does the problematic file
(/isilon/scratch/NS-081016/work/mutect2/1/NTP16-003495M-1_0_36932509.vcf.gz)
look like? The Java environment has recently changed to support MuTect2, since
it requires Java 8, so I suspect something is problematic there but the error
message you're seeing isn't enough to diagnose the problem. It's finding a
symptom (a corrupted/empty/problematic file) caused by something else during
the MuTect2 run.

Hope this helps with diagnosing the issues,
Brad

[Ivan De Dios]

Hi Brad,

The issues seem to have resolved themselves after doing a data upgrade and switching the default jre to oracle java 7 instead of openjdk-8-jre.