Running function "main" of "regenie_test_associations" failed because of AppInternalError

[WeiChenPan]

Hi, everyone This is our first time to use UKB_RAP. We're running regenie for GWAS, the step 1 process was successful, but we encountered some problem during step 2 (below is the log file). Is there anyone having the same problem?

Options in effect: --step 2 \ --bgen ukb00000_c21_b0_v1.bgen \ --phenoFile Hematologic_malignancy_imputation.phe \ --bsize 200 \ --pThresh 0.05 \ --test additive \ --pred ukb_c1-22_GRCh38_full_analysis_set_plus_decoy_hla_merged_pred.list \ --gz \ --sample ukb00000_c21_b0_v1.sample \ --extract /home/dnanexus/gel_imputed_snps_data_qc_pass_HM.snplist \ --covarFile Hematologic_malignancy_imputation.phe \ --bt \ --spa \ --phenoColList Hematologic_malignancy_cc \ --covarColList sex,age,ethnic_background,alcohol_status,hypertension,ever_smoked,SBP,BMI,NLR,CRP \ --ref-first \ --htp ukb00000_c21_b0_v1 \ --out ukb00000_c21_b0_v1 Association testing mode with fast multithreading using OpenMP

• bgen : [ukb00000_c21_b0_v1.bgen] -summary : bgen file (v1.2 layout, zstd compressed) with 488315 anonymous samples and 4376829 variants with 8-bit encoding. -index bgi file [ukb00000_c21_b0_v1.bgen.bgi] ERROR: BGenError Traceback (most recent call last): File "/home/dnanexus/job-GfKBQ7QJ3ZvYYY5Y9z3QffzY", line 39, in exec_code(job_code, _code_filename) File "/home/dnanexus/job-GfKBQ7QJ3ZvYYY5Y9z3QffzY", line 25, in exec_code exec(compiled_code, globals()) File "/home/dnanexus/job-GfKBQ7QJ3ZvYYY5Y9z3QffzY.code.py", line 208, in dxpy.run() File "/usr/local/lib/python3.8/dist-packages/dxpy/utils/exec_utils.py", line 150, in run result = ENTRY_POINT_TABLEjob['function'] File "/home/dnanexus/job-GfKBQ7QJ3ZvYYY5Y9z3QffzY.code.py", line 103, in main docker.run(cmd) File "/usr/lib/python3/dist-packages/sugar/dockertools.py", line 347, in run self._handle_last_process_cpe(cpe) File "/usr/lib/python3/dist-packages/sugar/dockertools.py", line 368, in _handle_last_process_cpe raise cpe File "/usr/lib/python3/dist-packages/sugar/dockertools.py", line 337, in run self._last_process = processing.run( File "/usr/lib/python3/dist-packages/sugar/processing/init.py", line 122, in run processes.block() File "/usr/lib/python3/dist-packages/sugar/processing/core.py", line 462, in block self.raise_if_error() File "/usr/lib/python3/dist-packages/sugar/processing/core.py", line 576, in raise_if_error raise CalledProcessError(self.returncode, str(self), output=msg) subprocess.CalledProcessError: Command 'docker run -e PYTHONUNBUFFERED=s -v /home/dnanexus:/home/dnanexus -w /home/dnanexus --rm dnanexus/regenie:latest bash -c 'regenie --step 2 --bgen ukb00000_c21_b0_v1.bgen --phenoFile Hematologic_malignancy_imputation.phe --bsize 200 --pThresh 0.05 --test additive --pred ukb_c1-22_GRCh38_full_analysis_set_plus_decoy_hla_merged_pred.list --gz --sample ukb00000_c21_b0_v1.sample --extract /home/dnanexus/gel_imputed_snps_data_qc_pass_HM.snplist --covarFile Hematologic_malignancy_imputation.phe --bt --spa --phenoColList Hematologic_malignancy_cc --covarColList sex,age,ethnic_background,alcohol_status,hypertension,ever_smoked,SBP,BMI,NLR,CRP --ref-first --htp ukb00000_c21_b0_v1 --out ukb00000_c21_b0_v1'' returned non-zero exit status 1. Close

[anastazie-dnanexus]

Hello, @WeiChenPan is there any specific reason why you were running REGENIE steps separatelyand not as one step using DNAnexus regenie app? I am assuming that you are using REGENIE app Step 1 and Step 2 or you were running REGENIE in Swiss Army Knife or cloudworkstation/ttyd/Jupyterlab?

[oklempir-cf]

Another idea - I am seeing that the error message "ERROR: BGenError" appeared just after it printed out the line -index bgi file [ukb00000_c21_b0_v1.bgen.bgi]. If I am not mistaken, I am not seeing bgen index file as an input to step 2. Could this fact be that reason for job failure?

[WeiChenPan]

@anastazie-dnanexus @oklempir-cf We've already solved the problem. The error is because the current .bgi index files for GEL BGEN data were created using a different version of the BGEN files, therefore, it caused the error while reading. So, the resolution is to create new .bgi files by using the swiss-army-knife app through the RAP.