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Structural Variation Discovery Pipeline error


I am attempting to use the Structural Variation Discovery Pipeline on hg38 aligned CRAM and BAM files, and am encountering the following error:

19/02/21 15:59:41 ERROR Executor: Exception in task 2093.0 in stage 5.0 (TID 12988)
java.lang.IllegalArgumentException: provided start is negative: -5

I have followed the recommendations on a previous thread "StructuralVariationDiscoveryPipelineSpark" , but continue to have the error. I am using resources from the GATK bundle and the following commands to run the tool:

gatk StructuralVariationDiscoveryPipelineSpark \
-I $BAM \
-R Homo_sapiens_assembly38.fasta \
-L wgs_calling_regions.hg38.interval_list \
--aligner-index-image hg38.fasta.img \
--kmers-to-ignore kmers_to_ignore_hg38.txt \
--contig-sam-file ${base}_aligned_contigs.sam \
-O ${base}_GATK_SV.vcf

The input BAM file has no errors by ValidateSamFile. Any help would be greatly appreciated! Thank you!


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