Intel MKL ERROR: Parameter 4 was incorrect on entry to DLASCL.

Hello, I have some problems when I run the gwas_summary_imputation.py.

Here is my script:

python ~/summary-gwas-imputation/src/gwas_summary_imputation.py \
                        -by_region_file ~/data_set/eur_ld.bed.gz \
                        -gwas_file 01.gwas_parsing.test.txt.gz \
                        -parquet_genotype ~/data_set/reference_panel_1000G/chr13.variants.parquet \
                        -parquet_genotype_metadata ~/data_set/reference_panel_1000G/variant_metadata.parquet \
                        -window 100000 \
                        -parsimony 7 \
                        -chromosome 13\
                        -regularization 0.1 \
                        -frequency_filter 0.01 \
                        -sub_batches 10 \
                        -sub_batch 0 \
                        --standardise_dosages \
                        -output ~/chr13_sb0_reg0.1_ff0.01_by_region.txt.gz

Here is the error:

INFO - Beginning process
INFO - Creating context by variant
INFO - Loading study
INFO - Loading variants' parquet file
INFO - Loading variants metadata
Level 9 - Loading row group 2
/home/hx37930/Miniconda3/envs/imlabtools/lib/python3.7/site-packages/pyarrow/pandas_compat.py:752: FutureWarning: .labels was deprecated in version 0.24.0. Use .codes instead.
  labels, = index.labels
INFO - Loading regions
Level 9 - Selecting target regions with specific chromosome
Level 9 - Selecting target regions from sub-batches
Level 9 - generating GWAS whitelist
INFO - Loading gwas
INFO - Acquiring filter tree for 223176 targets
INFO - Processing gwas source
Level 9 - Loaded 73743 GWAS variants
Level 9 - Parsing GWAS
Level 9 - Processing region 1/13 [18479.0, 1400095.0]
Level 8 - Roll out imputation
Level 8 - Preparing data
Level 8 - Performing imputation
Level 8 - Postprocessing
Level 8 - Palindromic Post processing
Level 9 - Processing region 2/13 [1400095.0, 2950436.0]
Level 8 - Roll out imputation
Level 8 - Preparing data
Level 8 - Performing imputation

Intel MKL ERROR: Parameter 4 was incorrect on entry to DLASCL.
INFO - Error for region (3,1400095.0,2950436.0): LinAlgError('SVD did not converge')

Could you help me solve this problem?

Thanks! Huifang

hakyimlab / MetaXcan

Intel MKL ERROR: Parameter 4 was incorrect on entry to DLASCL. #144