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[ec2-user@ip-172-31-22-48 data]$ docker run \
     --rm \
     --mount type=bind,src=/shared/data/libd/eqtl/data/,dst=/data \
     -t bryancquach/matrix_eqtl:2.2 \
     Rscript /opt/run_matrix_eqtl.R \
         --omic_data_file /data/gene_expression/libd_nac_aa_matrix_eqtl_input_gene_counts_case_only.txt \
         --snp_file /data/genotypes/smoking_cases/libd_nac_eqtl_genotypes_aa_chr22.txt \
         --output_prefix /data/results/test_tmp \
         --model linear \
         --cov_file /data/covariates/libd_nac_smoking_cases_aa_covariates_with_counts_based_peer_factors.txt \
         --omic_coordinates_file /data/gene_locations/libd_nac_aa_matrix_eqtl_input_gene_locations.txt \
         --snp_coordinates_file /data/snp_locations/libd_eqtl_snp_locations_chr22.txt \
         --cis \
         --cis_size 100 \
         --pval_threshold 1 \
         --batch_size 10000 \
         --no_fdr \
         --normalize rint

Model type:  linear
Loading data from tmp/omic_data_141f6bab6.txt ...Rows read: 10,000
Rows read: 20,000
Rows read: 21947 done.
Done.
Loaded data matrix with 21947 rows and 24 columns.
Loading data from /data/genotypes/smoking_cases/libd_nac_eqtl_genotypes_aa_chr22.txt ...Rows read: 10,000
Rows read: 20,000
Rows read: 30,000
Rows read: 40,000
Rows read: 50,000
Rows read: 60,000
Rows read: 70,000
Rows read: 80,000
Rows read: 90,000
Rows read: 100,000
Rows read: 110,000
Rows read: 120,000
Rows read: 130,000
Rows read: 140,000
Rows read: 150,000
Rows read: 158901 done.
Done.
Loaded data matrix with 158901 rows and 24 columns.
Loading data from /data/covariates/libd_nac_smoking_cases_aa_covariates_with_counts_based_peer_factors.txt ...Rows read: 15 done.
Done.
Loaded data matrix with 15 rows and 24 columns.
Matching data files and location files
21947of21947 genes matched
158901of158901 SNPs matched

Task finished in 0.106 seconds
Reordering genes

Task finished in 0.236000000000001 seconds
Processing covariates
Task finished in 0.00200000000000067 seconds
Processing gene expression data (imputation, residualization)
Task finished in 0.0169999999999995 seconds
Creating output file(s)
Task finished in 0.00999999999999979 seconds
Performing eQTL analysis
 2.08% done, 6,278 cis-eQTLs
 8.33% done, 10,634 cis-eQTLs
14.58% done, 15,247 cis-eQTLs
20.83% done, 20,841 cis-eQTLs
27.08% done, 26,507 cis-eQTLs
33.33% done, 33,882 cis-eQTLs
39.58% done, 41,241 cis-eQTLs
45.83% done, 44,001 cis-eQTLs
52.08% done, 48,738 cis-eQTLs
58.33% done, 55,900 cis-eQTLs
64.58% done, 62,528 cis-eQTLs
70.83% done, 69,441 cis-eQTLs
77.08% done, 74,309 cis-eQTLs
83.33% done, 77,819 cis-eQTLs
89.58% done, 80,158 cis-eQTLs
95.83% done, 83,501 cis-eQTLs
Error in saver.cis$getResults(gene, snps, n.tests.cis) :
  unused arguments (gene, snps, n.tests.cis)
Calls: Matrix_eQTL_main
Execution halted