java.lang.AssertionError: SAM dictionaries are not the same: SAMSequenceRecord(name=chrM,length=16571,dict_index=0,assembly=hg19) was found when SAMSequenceRecord(name=chr1,length=249250621,dict_index=0,assembly=null) was expected.

sourceforge.net | 4 months ago
  1. 0

    SAM tools / Mailing Lists

    ehc.ac | 1 year ago
    java.lang.AssertionError: SAM dictionaries are not the same: SAMSequenceRecord(name=chrM,length=16571,dict_index=0,assembly=hg19) was found when SAMSequenceRecord(name=chr1,length=249250621,dict_index=0,assembly=null) was expected.
  2. 0

    SAM tools / Mailing Lists

    sourceforge.net | 8 months ago
    java.lang.AssertionError: SAM dictionaries are not the same: SAMSequenceRecord(name=chrM,length=16571,dict_index=0,assembly=hg19) was found when SAMSequenceRecord(name=chr1,length=249250621,dict_index=0,assembly=null) was expected.
  3. 0

    SAM tools / Mailing Lists

    sourceforge.net | 3 months ago
    java.lang.AssertionError: SAM dictionaries are not the same: SAMSequenceRecord(name=chrM,length=16571,dict_index=0,assembly=hg19) was found when SAMSequenceRecord(name=chr1,length=249250621,dict_index=0,assembly=null) was expected.
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  5. 0

    SAM tools / Mailing Lists

    sourceforge.net | 4 months ago
    java.lang.AssertionError: SAM dictionaries are not the same: SAMSequenceRecord(name=chrM,length=16571,dict_index=0,assembly=hg19) was found when SAMSequenceRecord(name=chr1,length=249250621,dict_index=0,assembly=null) was expected.
  6. 0

    Errors about contigs in BAM or VCF files not being properly ordered or sorted — GATK-Forum

    broadinstitute.org | 2 months ago
    java.lang.IllegalArgumentException: java.lang.AssertionError: SAM dictionaries are not the same: SAMSequenceRecord(name=chrM,length=16571,dict_index=0,assembly=hg19) was found when SAMSequenceRecord(name=chr1,length=249250621,dict_index=0,assembly=null) was expected.

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    Root Cause Analysis

    1. java.lang.AssertionError

      SAM dictionaries are not the same: SAMSequenceRecord(name=chrM,length=16571,dict_index=0,assembly=hg19) was found when SAMSequenceRecord(name=chr1,length=249250621,dict_index=0,assembly=null) was expected.

      at picard.vcf.SortVcf.collectFileReadersAndHeaders()
    2. picard.vcf
      SortVcf.doWork
      1. picard.vcf.SortVcf.collectFileReadersAndHeaders(SortVcf.java:112)
      2. picard.vcf.SortVcf.doWork(SortVcf.java:81)
      2 frames