search

Illumina / Nirvana

The nimble & robust variant annotator
https://illumina.github.io/NirvanaDocumentation/
GNU General Public License v3.0
170 stars 44 forks source link

Input string was not in a correct format #51

Closed AdamuUu closed 2 years ago

AdamuUu commented 3 years ago

Could you help me with this one? What I run:

dotnet /home/adam/soft/nirvana/Nirvana/bin/Release/netcoreapp2.1/Nirvana.dll \
     --cache /home/adam/Pulpit/S5/covid_anno/Data/Cache/SARS-CoV-2/SARS-CoV \
     --sd /home/adam/Pulpit/S5/covid_anno/Data/SupplementaryAnnotation/SARS-CoV-2 \
     --ref /home/adam/Pulpit/S5/covid_anno/Data/References/SARS-CoV-2.ASM985889v3.dat \
     --in /home/adam/Pulpit/S5/samtools/RNA_IN_RG_bwa.vcf.gz \
     --out /home/adam/Pulpit/S5/samtools/RNA_IN_vars_anno

What I get:

---------------------------------------------------------------------------
Nirvana                                             (c) 2020 Illumina, Inc.
Stromberg, Roy, Lajugie, Jiang, Li, and Kang                         3.13.0
---------------------------------------------------------------------------

Initialization                                         Time     Positions/s
---------------------------------------------------------------------------
Cache                                               00:00:00.0

ERROR: Input string was not in a correct format.

Stack trace:
   at System.Number.ParseDouble(ReadOnlySpan`1 value, NumberStyles options, NumberFormatInfo numfmt)
   at System.Double.Parse(String s)
   at System.Linq.Enumerable.SelectArrayIterator`2.ToArray()
   at MitoHeteroplasmy.MitoHeteroplasmyReader.GetProvider() in /home/adam/soft/nirvana/Nirvana/MitoHeteroplasmy/MitoHeteroplasmyReader.cs:line 42
   at Nirvana.AnnotationResources..ctor(String refSequencePath, String inputCachePrefix, List`1 saDirectoryPaths, List`1 customAnnotations, String customStrTsvPath, Boolean disableRecomposition, Boolean forceMitochondrialAnnotation, Boolean useLegacyVids, PerformanceMetrics metrics) in /home/adam/soft/nirvana/Nirvana/Nirvana/AnnotationResources.cs:line 75
   at Nirvana.Nirvana.GetAnnotationResources() in /home/adam/soft/nirvana/Nirvana/Nirvana/Nirvana.cs:line 52
   at Nirvana.Nirvana.ProgramExecution() in /home/adam/soft/nirvana/Nirvana/Nirvana/Nirvana.cs:line 34
   at CommandLine.Builders.ConsoleAppErrors.Execute(Func`1 executeMethod) in /home/adam/soft/nirvana/Nirvana/CommandLine/Builders/ConsoleAppBuilder.cs:line 162
MichaelStromberg commented 3 years ago

Hi Adam, that's an interesting one. The MitoHeteroplasmy data source is embedded in Nirvana and we can't come up with a reason why this would suddenly fail. We see that the MitoHeteroplasmyReader has been unchanged since October 2020 and has been used on hundreds of thousands of VCFs.

Having said that, I see that you're running Nirvana 3.13. Did you compile it on your own or did you use the pre-compiled binaries that we posted in GitHub?

In the meantime, I'll try analyzing some COVID-19 VCFs using both Nirvana 3.13 and 3.14 to see if I can reproduce the error.

MichaelStromberg commented 3 years ago

Hi Adam,

Since I didn't have the VCF that you used, I went ahead and used the COVID-19 VCF provided on our documentation site

I used the precompiled binaries for both 3.13 and 3.14 and everything worked well. You can find the precompiled binaries for Nirvana 3.14 here: https://github.com/Illumina/Nirvana/releases/tag/v3.14.0 (look in the assets section)

AdamuUu commented 3 years ago

Hi Michael,

Thank you so much for help and support!

Best Regards, Adam

czw., 29 kwi 2021 o 23:13 Michael Strömberg @.***> napisał(a):

Hi Adam,

Since I didn't have the VCF that you used, I went ahead and used the COVID-19 VCF https://illumina.github.io/NirvanaDocumentation/files/Covid19Mutations.vcf.gz provided on our documentation site https://illumina.github.io/NirvanaDocumentation/introduction/covid19/

I used the precompiled binaries for both 3.13 and 3.14 and everything worked well. You can find the precompiled binaries for Nirvana 3.14 here: https://github.com/Illumina/Nirvana/releases/tag/v3.14.0 (look in the assets section)

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/Illumina/Nirvana/issues/51#issuecomment-829599891, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKPMCZD7V2JX3VA6JPAP5YTTLHDWDANCNFSM43SU4JAA .