R script error associated with singular value decomposition?
Hello, I've run into the below error while running DBGWAS using Singularity. I've skipped step 1 in this case, as there were memory issues that have have been negated by splitting the job into its individual steps. The error seems to be associated with singular value decomposition and the R script? Do you have any idea what's gone wrong please?
Code: run_dbgwas -strains bugs_phenotype_dataset/strains -newick bugs_phenotype_dataset/strains.newick -nc-db Resistance_DB_for_DBGWAS.fasta -pt-db uniprot_sprot_bacteria_for_DBGWAS.fasta -nb-cores 10 -verbose 1 -skip1
Results and error:
Step 1. Building DBG and mapping strains on the DBG...
Skipping Step 1!
build_dbg
map_reads
Done!
Step 2. Running statistical test (bugwas + gemma)...
Executing Rscript --vanilla /dbgwas/bin/DBGWAS_lib//DBGWAS.R /dbgwas/bin/DBGWAS_lib/ /ab54/db45/ell/analysis_/dbgwas/phenotype_2/output/step1 /ab54/db45/ell/analysis_/dbgwas/phenotype_2/output/step1/bugwas_input.id_phenotype bugwas_out /dbgwas/bin/DBGWAS_lib//gemma.0.93b 0.01 /ab54/db45/ell/analysis_/dbgwas/phenotype_2/bugs_phenotype_dataset/strains.newick 2>&1...
During startup - Warning messages:
1: Setting LC_CTYPE failed, using "C"
2: Setting LC_COLLATE failed, using "C"
3: Setting LC_TIME failed, using "C"
4: Setting LC_MESSAGES failed, using "C"
5: Setting LC_MONETARY failed, using "C"
6: Setting LC_PAPER failed, using "C"
7: Setting LC_MEASUREMENT failed, using "C"
[DBGWAS] Reading unitigs from /ab54/db45/ell/analysis_/dbgwas/phenotype_2/output/step1/bugwas_input.unique_rows.binary
[DBGWAS] Reading phenotypes from /ab54/db45/ell/analysis_/dbgwas/phenotype_2/output/step1/bugwas_input.id_phenotype
[DBGWAS] Preparing tree for lineage effect analysis from /ab54/db45/ell/analysis_/dbgwas/phenotype_2/bugs_phenotype_dataset/strains.newick
[DBGWAS] Restricting genotype 4198013/5594886 patterns with MAF >= 0.01.
[DBGWAS] Building kinship matrix
Get kinship matrix
Reading Files ...
-## number of total individuals = 2515
-## number of analyzed individuals = 2515
-## number of covariates = 1
-## number of total SNPs = 4719719
-## number of analyzed SNPs = 4719719
Calculating Relatedness Matrix ...
Reading SNPs 0.00%
Reading SNPs = 2.12%
Reading SNPs == 4.24%
Reading SNPs === 6.36%
Reading SNPs ==== 8.48%
Reading SNPs ===== 10.59%
Reading SNPs ====== 12.71%
Reading SNPs ======= 14.83%
Reading SNPs ======== 16.95%
Reading SNPs ========= 19.07%
Reading SNPs ========== 21.19%
Reading SNPs =========== 23.31%
Reading SNPs ============ 25.43%
Reading SNPs ============= 27.54%
Reading SNPs ============== 29.66%
Reading SNPs =============== 31.78%
Reading SNPs ================ 33.90%
Reading SNPs ================== 36.02%
Reading SNPs =================== 38.14%
Reading SNPs ==================== 40.26%
Reading SNPs ===================== 42.38%
Reading SNPs ====================== 44.49%
Reading SNPs ======================= 46.61%
Reading SNPs ======================== 48.73%
Reading SNPs ========================= 50.85%
Reading SNPs ========================== 52.97%
Reading SNPs =========================== 55.09%
Reading SNPs ============================ 57.21%
Reading SNPs ============================= 59.33%
Reading SNPs ============================== 61.44%
Reading SNPs =============================== 63.56%
Reading SNPs ================================ 65.68%
Reading SNPs ================================= 67.80%
Reading SNPs ================================== 69.92%
Reading SNPs ==================================== 72.04%
Reading SNPs ===================================== 74.16%
Reading SNPs ====================================== 76.28%
Reading SNPs ======================================= 78.39%
Reading SNPs ======================================== 80.51%
Reading SNPs ========================================= 82.63%
Reading SNPs ========================================== 84.75%
Reading SNPs =========================================== 86.87%
Reading SNPs ============================================ 88.99%
Reading SNPs ============================================= 91.11%
Reading SNPs ============================================== 93.23%
Reading SNPs =============================================== 95.34%
Reading SNPs ================================================ 97.46%
Reading SNPs ================================================= 99.58%
Reading SNPs ==================================================100.00%
[DBGWAS] Performing association tests
Rescaled variants.
Error in La.svd(x, nu, nv) :
BLAS/LAPACK routine 'DLASCL' gave error code -4
Calls: cdbg_lin_loc -> svd -> La.svd
Execution halted
[FATAL ERROR] Error executing Rscript --vanilla /dbgwas/bin/DBGWAS_lib//DBGWAS.R /dbgwas/bin/DBGWAS_lib/ /ab54/db45/ell/analysis_/dbgwas/phenotype_2/output/step1 /ab54/db45/ell/analysis_/dbgwas/phenotype_2/output/step1/bugwas_input.id_phenotype bugwas_out /dbgwas/bin/DBGWAS_lib//gemma.0.93b 0.01 /ab54/db45/ell/analysis_/dbgwas/phenotype_2/bugs_phenotype_dataset/strains.newick 2>&1. Exit status: 256