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Parse error in interval list header #2355

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heuermh opened this issue Mar 8, 2022 · 0 comments · Fixed by #2356
Closed

Parse error in interval list header #2355

heuermh opened this issue Mar 8, 2022 · 0 comments · Fixed by #2356

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@heuermh
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heuermh commented Mar 8, 2022

scala> val references = sc.loadSequenceDictionary("references/Homo_sapiens/GATK/GRCh38/
Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict")
...
scala> val features = sc.loadFeatures("references/Homo_sapiens/GATK/GRCh38/Annotation/
intervals/wgs_calling_regions.hg38.interval_list", optSequenceDictionary = Some(references))
...
org.apache.spark.SparkException: Job aborted due to stage failure: Task 2 in stage 0.0 failed 1
times, most recent failure: Lost task 2.0 in stage 0.0 (TID 2) (10.10.4.241 executor driver):
java.lang.Exception: Expected fields of the form 'key:value' in field sapiens but got:
[Ljava.lang.String;@4542b1b0. Line:
@SQ     SN:chrUn_JTFH01000886v1_decoy   LN:1064 M5:5ad23055bdc140edb211af99bf7d76e3
     AS:38   UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta   
SP:Homo sapiens
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