Open charbel-gem opened 3 years ago
That's interesting. Unfortunately, without the VCF line that triggered the issue, it's difficult to debug. If you could share a VCF line (or a sanitized version of a VCF line that still causes the issue), we can figure out what is going on.
That's interesting. Unfortunately, without the VCF line that triggered the issue, it's difficult to debug. If you could share a VCF line (or a sanitized version of a VCF line that still causes the issue), we can figure out what is going on.
Sorry for that, here's a full screenshot of the error message. It's only 1 line, and it's actually the second variant in the VCF file.
Thanks Charbel, I'll take a look at this today.
Hi Charbel, it looks like the core issue was the reference sequence name.
Using a VCF that looks like this worked fine:
##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##contig=<ID=NC_045512.2,length=29903>
#CHROM POS ID REF ALT QUAL FILTER INFO
NC_045512.2 3037 . C T . PASS .
Here's the resulting console output:
---------------------------------------------------------------------------
Nirvana (c) 2020 Illumina, Inc.
Stromberg, Roy, Lajugie, Jiang, Li, and Kang 3.14.0-0-g19868c36
---------------------------------------------------------------------------
Initialization Time Positions/s
---------------------------------------------------------------------------
Cache 00:00:00.0
SA Position Scan 00:00:00.0 86
Reference Preload Annotation Variants/s
---------------------------------------------------------------------------
NC_045512 00:00:00.0 00:00:00.0 10
Summary Time Percent
---------------------------------------------------------------------------
Initialization 00:00:00.0 10.4 %
Preload 00:00:00.0 0.0 %
Annotation 00:00:00.0 17.0 %
Peak memory usage: 63.5 MB
Time: 00:00:00.4
Hi Charbel,
Since other people might end up having similar reference naming issues, I updated the Nirvana COVID-19 files to accept NC_045512v2 as a synonym for NC_045512.2. Just grab the latest data pack from here: https://illumina.github.io/NirvanaDocumentation/files/Covid19Data.zip
Best regards,
// Michael
Hello.
I'm facing the following error while trying to run the program on a VCF file of mine:
ERROR: Object reference not set to an instance of an object
. However, the tool is working normally when used with the example VCF file downloaded from the tool's manual page. Please check this link for a screenshot of the errorNote that I'm trying to annotate a COVID-19 vcf file, following the steps here
What could be the issue?