Greetings all. I am trying to run VEP within Hail with just:
mt_vep = hl.vep(mt, <VEP json file>)
and I am running into this issue:
FatalError: JsonParseException: Non-standard token 'NaN': enable JsonParser.Feature.ALLOW_NON_NUMERIC_NUMBERS to allow
at [Source: UNKNOWN; line: 1, column: 407]
Java stack trace:
org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 43.0 failed 1 times, most recent failure: Lost task 0.0 in stage 43.0 (TID 111): com.fasterxml.jackson.core.JsonParseException: Non-standard token 'NaN': enable JsonParser.Feature.ALLOW_NON_NUMERIC_NUMBERS to allow
at [Source: (String)"{"most_severe_consequence":"5_prime_UTR_variant","regulatory_feature_consequences":[{"variant_allele":"G","regulatory_feature_id":"ENSR00001309607","impact":"MODIFIER","minimised":1,"allele_num":1,"consequence_terms":["regulatory_region_variant"],"biotype":"promoter"}],"assembly_name":"GRCh38","id":"9_98056788_T/G","transcript_consequences":[{"consequence_terms":["5_prime_UTR_variant"],"gene_symbol":NaN,"protein_id":"ENSP00000210444","uniparc":"UPI000013597F","cdna_start":50,"biotype":"protein_c"[truncated 2108 chars]; line: 1, column: 407]
Can this be solved within Hail? (i.e. specifying some parameters for spark_conf?) I have not seen this issue before and I am not too sure how to approach it. Appreciate any comments.