SAIGE

A tool to perform genome-wide association tests in large-scale data sets and biobanks

Troubleshooting

For general tips on troubleshooting, see guide.

Issue Example error message What to do

Issue	Example error message	What to do
Issue with input	`Value provided for input field "" could not be parsed as file: could not resolve "" to a name or ID`	Check that the input file path you specified is correct
Error fitting null model (Step 1)	`cannot stat '/home/dnanexus/*.sparseSigma.mtx: No such file or directory`	In SAIGE GWAS GRM app, set `Is Sparse K In` = True. This parameter can be found in the SAIGE-GENE section
SPAGMMAT test error (Step 2)	`Error in SPAGMMATtest(vcfFile = opt$vcfFile, vcfFileIndex = opt$vcfFileIndex, :` `467880 samples have been used to fit the glmm null model` `chromosome 0 is out of the range of null model LOCO results`	Specify "--chr" under the input "Extra Options". See the following github issue.

Issue with input

Value provided for input field "" could not be parsed as file: could not resolve "" to a name or ID

Check that the input file path you specified is correct

Error fitting null model (Step 1)

cannot stat '/home/dnanexus/*.sparseSigma.mtx: No such file or directory

In SAIGE GWAS GRM app, set Is Sparse K In = True. This parameter can be found in the SAIGE-GENE section

SPAGMMAT test error (Step 2)

Error in SPAGMMATtest(vcfFile = opt$vcfFile, vcfFileIndex = opt$vcfFileIndex, :

467880 samples have been used to fit the glmm null model

chromosome 0 is out of the range of null model LOCO results

Specify "--chr" under the input "Extra Options".

See the following github issue.

Last updated 6 months ago