ReorderSam: New reference sequence does not contain a matching contig for ERCC-00002

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Cora Olpe

• October 03, 2023 08:25

I am running ReorderSam to try and match my bam files to the order of the reference but it looks like they are in the same order, but somehow the reference (Mus_musculus.GRCm38.dna.primary_assembly.dict)

is lacking the contig ERCC-00002. Because of this issue I cannot proceed with my pipeline (SplitNCigarReads fails) 

 

My code is:

for fn in $(find /home/colpe/scratch/raw_data/marked_dup/ -name "*.bam")

do

gatk ReorderSam -I "$fn" -O /home/colpe/scratch/raw_data/marked_reordered/"$(basename $fn)"_reordered.bam -SD /home/colpe/data/ref_sequences/Mus_musculus.GRCm38.dna.primary_assembly.dict

done

The error I get is:

picard.PicardException: New reference sequence does not contain a matching contig for ERCC-00002

Should I just remove this contig from my bam files?

0

• 

  Gökalp Çelik

  • October 03, 2023 08:48

  Hi again. 

  The response that we provided to you is still valid in this case. 

  https://gatk.broadinstitute.org/hc/en-us/community/posts/19250645718171-SplitNCigarReads-Contig-ERCC-ERCC-00002-given-as-location-but-this-contig-isn-t-present-in-the-Fasta-sequence-dictionary?page=1#community_comment_19276884014107 

  One thing that can be done to save your time would to obtain that additional contig and adding that contig to your reference genome if all other contigs already match with their names, aliases and md5 hashes. 

  I hope this helps. 

   

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