htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 1787: The reference allele cannot be missing

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Solutions on the web

via GitHub by ooliynyk
, 1 year ago
The provided VCF file is malformed at approximately line number 1787: The reference allele cannot be missing
via GitHub by inti
, 2 years ago
The provided VCF file is malformed at approximately line number 108: unparsable vcf record with allele S, for input source: /media/TeraData/ipedroso/ANALYSES/DEKKERA/variation/AWRI1499_ref/awri1499_vsawri1499Ref/work/freebayes/AWRI1499_contig1_scaffold1/1-AWRI1499_contig1_scaffold1_0_12137.vcf.gz
via GitHub by inti
, 2 years ago
The provided VCF file is malformed at approximately line number 88: empty alleles are not permitted in VCF records
via GitHub by razZ0r
, 10 months ago
The provided VCF file is malformed at approximately line number 54693: BUG: log10PError cannot be > 0 : 1.0, for input source: /pico/scra tch/userexternal/esebesty/bcbio_run/uuid_batch5932/work/vardict/21/LUAD_5932-21_0_41399576.vcf.gz
via GitHub by whitejbiii
, 2 years ago
The provided VCF file is malformed at approximately line number 649: unparsable vcf record with allele *, for input source: /media/jawhite/Data/662-exome-trio/work/joint/gatk-haplotype-joint/trio-bwa-j/1/trio-bwa-j-1_0_15543565.vcf.gz
via GitHub by heuermh
, 9 months ago
The provided VCF file is malformed at approximately line number 15364: Duplicate allele added to VariantContext: C
htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 1787: The reference allele cannot be missing
at htsjdk.variant.vcf.AbstractVCFCodec.generateException(AbstractVCFCodec.java:783)
at htsjdk.variant.vcf.AbstractVCFCodec.checkAllele(AbstractVCFCodec.java:572)
at htsjdk.variant.vcf.AbstractVCFCodec.parseAlleles(AbstractVCFCodec.java:531)
at htsjdk.variant.vcf.AbstractVCFCodec.parseVCFLine(AbstractVCFCodec.java:336)
at htsjdk.variant.vcf.AbstractVCFCodec.decodeLine(AbstractVCFCodec.java:279)
at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:257)
at org.seqdoop.hadoop_bam.VCFRecordReader.nextKeyValue(VCFRecordReader.java:144)
at org.apache.spark.rdd.NewHadoopRDD$$anon$1.hasNext(NewHadoopRDD.scala:163)
at org.apache.spark.InterruptibleIterator.hasNext(InterruptibleIterator.scala:39)
at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371)
at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371)
at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1$$anonfun$12$$anonfun$apply$4.apply$mcV$sp(PairRDDFunctions.scala:1034)
at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1$$anonfun$12$$anonfun$apply$4.apply(PairRDDFunctions.scala:1034)
at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1$$anonfun$12$$anonfun$apply$4.apply(PairRDDFunctions.scala:1034)
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1206)
at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1$$anonfun$12.apply(PairRDDFunctions.scala:1042)
at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1$$anonfun$12.apply(PairRDDFunctions.scala:1014)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:66)
at org.apache.spark.scheduler.Task.run(Task.scala:88)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)

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