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

Truncated supplementary data source files #42

Closed junyanzho closed 3 years ago

junyanzho commented 3 years ago

I try to annotate variants of VCF( including 3589 SNPs), encounter ERROR as below:

Nirvana (c) 2020 Illumina, Inc. Stromberg, Roy, Lajugie, Jiang, Li, and Kang 3.13.0-0-ga57e78a7

Initialization Time Positions/s

Cache 00:00:01.9 SA Position Scan 00:00:00.9 3,710

Reference Preload Annotation Variants/s

chr1 00:00:10.6 00:00:03.7 114 chr2 00:00:09.7 00:00:03.2 82 chr3 00:00:08.0 00:00:02.7 72 chr4 00:00:03.6 00:00:02.3 73

ERROR: Unable to read beyond the end of the stream.

Stack trace: at System.IO.BinaryReader.ReadByte() at IO.ExtendedBinaryReader.ReadOptInt32() in D:\Projects\Nirvana_3.13\IO\ExtendedBinaryReader.cs:line 46 at VariantAnnotation.NSA.NsaBlock.Read(ExtendedBinaryReader reader) in D:\Projects\Nirvana_3.13\VariantAnnotation\NSA\NsaBlock.cs:line 41 at VariantAnnotation.NSA.NsaReader.PreLoad(IChromosome chrom, List`1 positions) in D:\Projects\Nirvana_3.13\VariantAnnotation\NSA\NsaReader.cs:line 91 at System.Threading.ExecutionContext.RunInternal(ExecutionContext executionContext, ContextCallback callback, Object state) --- End of stack trace from previous location where exception was thrown --- at System.Threading.Tasks.Task.ExecuteWithThreadLocal(Task& currentTaskSlot)

Then, I split and annotate variants by chromosome. Annotation are completed with chromosome 1-4, annotation on other chromosomes(5-22, X) also failed with above ERROR.

Could you help me figure out what is wrong?

Thanks!

MichaelStromberg commented 3 years ago

Hi there,

This usually happens if one of the Supplementary Annotation data sources was truncated. One way of fixing this is to re-run the Downloader using the same output directory as you used before. This way, Nirvana will repair any truncated files that it finds.

Let me know if that works for you.

Besides that, this is reminding me that it would be incredibly helpful if Nirvana could indicate which Supplementary Annotation file was truncated (i.e. the one that triggered the ERROR: Unable to read beyond the end of the stream. exception.

junyanzho commented 3 years ago

We try to re-run downloader and test. It's OK now. Thanks for your help.

MichaelStromberg commented 3 years ago

Awesome! We're going to add some better debugging text to our error messages to make that easier in the future.

For curiosity, what do you think led to the truncated file? Did you run out of disk space or do you think there was an issue with the network connectivity? We're trying to identify how people are getting truncated files in an effort to improve our workflow.

junyanzho commented 3 years ago

In my situation, it was caused by network connection.