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Latest Clinvar release cannot be parsed

Open mattsolo1 opened this issue 3 years ago • 0 comments

Java stack trace:
org.apache.spark.SparkException: Job aborted due to stage failure: Task 1434 in stage 0.0 failed 20 times, most recent failure: Lost task 1434.20 in stage 0.0 (TID 2070) (vep85-sw-q2n2.c.gnomadev.internal executor 63): is.hail.utils.HailException: Caught exception while reading hdfs://vep85-m/tmp/clinvar_variants.tsv: is.hail.utils.HailException: could not convert "Un:113557" to locus<GRCh37> in column "locus_GRCh37" 
  offending line: Un:113557	["T", "A"]	chr4:190174726	["T", "A"]	{"clinvar_var...
Hail version: 0.2.81-edeb70bc789c
Error summary: HailException: Invalid locus 'Un:113557' found. Contig 'Un' is not in the reference genome 'GRCh37'.

[Stage 0:====================================================>(1999 + 6) / 2000]

mattsolo1 avatar Aug 02 '22 19:08 mattsolo1