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Illumina / Nirvana

The nimble & robust variant annotator
https://illumina.github.io/NirvanaDocumentation/
GNU General Public License v3.0
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Cytogenetic bands error when annotating COVID-19 VCF #49

Open charbel-gem opened 3 years ago

charbel-gem commented 3 years ago

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 error

Note that I'm trying to annotate a COVID-19 vcf file, following the steps here

What could be the issue?

MichaelStromberg commented 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.

charbel-gem commented 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.

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.

MichaelStromberg commented 3 years ago

Thanks Charbel, I'll take a look at this today.

MichaelStromberg commented 3 years ago

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
MichaelStromberg commented 3 years ago

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