ERROR while calling variants...

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Manoj Kumar

• May 10, 2020 03:23
• Edited

I am using gatk-4.1.7.0 version with following command, however I am getting error. please advice....

Command:

gatk-4.1.7.0$./gatk HaplotypeCaller -R /home/kumarm/allan-work/RNASEq-alignment/ref_sequence.fasta -I /home/kumarm/allan-work/RNASEq-alignment/sorted-out-align.bam.bai -O /home/kumarm/allan-work/RNASEq-alignment/raw_variants.vcf

ERROR:::

A USER ERROR has occurred: Input files reference and reads have incompatible contigs: No overlapping contigs found.
reference contigs = [KF267450.1]
reads contigs = []

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• 

  Bhanu Gandham

  • May 10, 2020 23:55

  Take a look at this doc: https://gatk.broadinstitute.org/hc/en-us/articles/360035891131-Errors-about-input-files-having-missing-or-incompatible-contigs

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  Manoj Kumar

  • May 11, 2020 03:35
  • Edited

  Hi I have fastq (MnION) file and a reference fasta file..I have still issue to not getting results ...... 

  --FILE 1

  @ID_5331388
  CTCCACTCTGGGATGGGAATTCTCCTCCACTCTGGGATGGGAATTCTCCTCCACTCTGGGATGGGAATTCTCCTCCACTCTGGGATGGGAATTCTCCTCC
  +ID_5331388
  AAFFFJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJ7FFJJJJJJJJJFJJJFJJJJJJJJJJJJJFJJJJJJJJJJJJJJJ
  @ID_6694963
  CTCCACTCTGGGATGGGAATTCTCCTCCACTCTGGGATGGGAATTCTCCTCCACTCTGGGCTGGGAATTCTCCTCCACTCTGGGATGGGCATTCTCCTCC
  +ID_6694963
  AAAFFJJJJJJJFJJJJJFJJFJJJJJJJJJJJJJJFJJJF<FJJJJJJJJJ-AJ<-AJF-7JFF7--7<7FFFJJ-<<AA-FF-<FAJ))-AF-----)

  ---FILE 2

  >KF267450.1
  TTAAAAGAGATTTTCTATCTACGGATAGTTAGCTCTTTTTCTAGACTCTTGTCTACTCAATTCAACTAAA
  CGAAATTTTGTCCTTCCGGCCGCATGTCCATGCTGCTGGAAGCTGACGTGGAATTTCATTAGGTTTGCTT

   

  --ERROR--

  A USER ERROR has occurred: Input files reference and reads have incompatible contigs: No overlapping contigs found.
  reference contigs = [KF267450.1]
  reads contigs = []

   

   

   

   

   

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