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AnnotateInsertedSequence cannot complete #554

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vragkousis opened this issue Dec 19, 2021 · 1 comment
Closed

AnnotateInsertedSequence cannot complete #554

vragkousis opened this issue Dec 19, 2021 · 1 comment

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@vragkousis
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Hello!

I am using virusbreakend with the default bwa aligner and I can't get past the AnnotateInsertedSequence step. Please let me know what this log file suggests the problem is.

virusbreakend.20211219_193215.OGpowerhouse.62447.log
@d-cameron
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Looks like you're missing /home/vragkousis/Desktop/Tools/Genomes/hg38.fa.dict. Running gridss -s setupreference -r /home/vragkousis/Desktop/Tools/Genomes/hg38.fa should create it.

d-cameron pushed a commit that referenced this issue Dec 23, 2021
#554 auto-generating GRIDSS reference files for the host reference
d499a27
d-cameron pushed a commit that referenced this issue Dec 23, 2021
#554 defaulting to external bwa alignment for all programs not just S…
d17bb06 
…oftClipsToSplitReads
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@d-cameron @vragkousis