Error in SnpSift tool due to token ANN interpretation and out of memory

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1

Can the below problem be solved? Kindly suggest.

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What the error means

Part of the message What it usually means in plain English
line 2:8 no viable alternative at input 'ANN' The filter expression you gave to SnpSift cannot be parsed. At line 2, column 8 the parser saw the token ANN and didn’t know how to interpret it.
java.lang.OutOfMemoryError: Java heap space While trying to process the VCF, Java ran out of memory (the “heap” that stores objects). This is typically seen when the input VCF is large or when the filter expression forces SnpSift to keep a lot of data in memory.

Both problems are independent, but they happen together because the tool tries to read the whole file, fails to parse the expression, and then exhausts its default memory allocation.
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2

it probably can be fixed, yes, but not based on an AI summary.

You can either:

  • submit a bug report directly from the failed job run, or
  • post the original error message plus the snpsift query you used here.
1 Like
3

How do I do the following?

  • submit a bug report directly from the failed job run, or
  • post the original error message plus the snpsift query you used here.
4

Like this: FAQ: Troubleshooting errors