Task JointGenotyping.ImportGVCFs failed with message 10: failed to copy files
Task JointGenotyping.ImportGVCFs failed on joint discovery of 34 exome samples:
When I look into the stderr.log file:
08:33:54.012 INFO GenomicsDBImport - Starting batch input file preload
08:33:59.013 INFO GenomicsDBImport - Finished batch preload
08:33:59.013 INFO GenomicsDBImport - Importing batch 1 with 34 samples
terminate called after throwing an instance of 'VCF2TileDBException'
what(): VCF2TileDBException : Incorrect cell order found - cells must be in column major order. Previous cell: [ 20, 664149855 ] current cell: [ 20, 664149855 ].
The most likely cause is unexpected data in the input file:
(a) A VCF file has two lines with the same genomic position
(b) An unsorted CSV file
(c) Malformed VCF file (or malformed index)
See point 2 at: https://github.com/Intel-HLS/GenomicsDB/wiki/Importing-VCF-data-into-GenomicsDB#organizing-your-data
GVCFs were called with haplotypecaller-gvcf-gatk4 (all done with workspace: Germline-SNPs-Indels-GATK4-hg38)
What can I do to fix this error?