Assuming unrestricted shared filesystem usage. None host: login-q-4 Building DAG of jobs... Your conda installation is not configured to use strict channel priorities. This is however important for having robust and correct environments (for details, see https://conda-forge.org/docs/user/tipsandtricks.html). Please consider to configure strict priorities by executing 'conda config --set channel_priority strict'. Creating conda environment workflow/envs/r.yaml... Downloading and installing remote packages. Cleaning up conda package tarballs. Environment for /rds/project/rds-4o5vpvAowP0/software/MitoImpute/workflow/envs/r.yaml created (location: .snakemake/conda/affd7974118e8caa2383ed3025b8c69b_) Using shell: /usr/bin/bash Provided cores: 3 Rules claiming more threads will be scaled down. Job stats: job count ------------- ------- FixChromName 1 Impute2 1 all 1 bplink2oxford 1 bplink2plink 1 oxford2bed 1 oxford2ped 1 oxford2vcf 1 plots 1 yri2rcrs_flip 1 total 10 Select jobs to execute... Execute 1 jobs... [Thu Aug 21 12:58:23 2025] localrule yri2rcrs_flip: input: resources/ReferencePanel_v1_example/ReferencePanelSNPs_MAFexample.txt, results/example/chrMT_example.bim output: results/example/chrMT_example_rcrsFlipped.bim log: results/example/logs/yri2rcrs_flip.log jobid: 7 reason: Missing output files: results/example/chrMT_example_rcrsFlipped.bim wildcards: dataout=results, sample=example resources: tmpdir=/rds/user/jhz22/hpc-work/work Activating conda environment: .snakemake/conda/affd7974118e8caa2383ed3025b8c69b_ [Thu Aug 21 12:58:28 2025] Finished jobid: 7 (Rule: yri2rcrs_flip) 1 of 10 steps (10%) done Select jobs to execute... Execute 2 jobs... [Thu Aug 21 12:58:28 2025] localrule bplink2plink: input: results/example/chrMT_example.bed, results/example/chrMT_example.bim, results/example/chrMT_example.fam, results/example/chrMT_example_rcrsFlipped.bim output: results/example/example_typedOnly.map, results/example/example_typedOnly.ped log: results/example/logs/bplink2plink.log jobid: 11 reason: Missing output files: results/example/example_typedOnly.ped, results/example/example_typedOnly.map; Input files updated by another job: results/example/chrMT_example_rcrsFlipped.bim wildcards: dataout=results, sample=example resources: tmpdir=/rds/user/jhz22/hpc-work/work Activating conda environment: .snakemake/conda/f1f716d4caa09fcf1c22c007af0ac109 [Thu Aug 21 12:58:28 2025] localrule bplink2oxford: input: results/example/chrMT_example.bed, results/example/chrMT_example.bim, results/example/chrMT_example.fam, results/example/chrMT_example_rcrsFlipped.bim output: results/example/example.gen, results/example/example.sample log: results/example/logs/bplink2oxford.log jobid: 4 reason: Missing output files: results/example/example.gen, results/example/example.sample; Input files updated by another job: results/example/chrMT_example_rcrsFlipped.bim wildcards: dataout=results, sample=example resources: tmpdir=/rds/user/jhz22/hpc-work/work Activating conda environment: .snakemake/conda/f1f716d4caa09fcf1c22c007af0ac109 [Thu Aug 21 12:58:29 2025] Finished jobid: 11 (Rule: bplink2plink) 2 of 10 steps (20%) done [Thu Aug 21 12:58:29 2025] Finished jobid: 4 (Rule: bplink2oxford) 3 of 10 steps (30%) done Removing temporary output results/example/chrMT_example.fam. Removing temporary output results/example/chrMT_example.bim. Removing temporary output results/example/chrMT_example.bed. Removing temporary output results/example/chrMT_example_rcrsFlipped.bim. Select jobs to execute... Execute 1 jobs... [Thu Aug 21 12:58:29 2025] localrule Impute2: input: resources/ReferencePanel_v1_example/ReferencePanel_v1_example_MtMap.txt, resources/ReferencePanel_v1_example/ReferencePanel_v1_example.hap.gz, resources/ReferencePanel_v1_example/ReferencePanel_v1_example.legend.gz, results/example/example.gen, results/example/example.sample output: results/example/example_imputed, results/example/example_imputed_samples, results/example/example_imputed_info log: results/example/logs/Impute2.log jobid: 3 reason: Missing output files: results/example/example_imputed_samples, results/example/example_imputed, results/example/example_imputed_info; Input files updated by another job: results/example/example.gen, results/example/example.sample wildcards: dataout=results, sample=example resources: tmpdir=/rds/user/jhz22/hpc-work/work Activating conda environment: .snakemake/conda/64a7633ce7105593cfd2eba11fe76683 [Thu Aug 21 12:58:40 2025] Finished jobid: 3 (Rule: Impute2) 4 of 10 steps (40%) done Removing temporary output results/example/example.gen. Removing temporary output results/example/example.sample. Select jobs to execute... Execute 1 jobs... [Thu Aug 21 12:58:40 2025] localrule FixChromName: input: results/example/example_imputed output: results/example/example_imputed_ChromFixed jobid: 2 reason: Missing output files: results/example/example_imputed_ChromFixed; Input files updated by another job: results/example/example_imputed wildcards: dataout=results, sample=example resources: tmpdir=/rds/user/jhz22/hpc-work/work Activating conda environment: .snakemake/conda/f1f716d4caa09fcf1c22c007af0ac109 [Thu Aug 21 12:58:40 2025] Finished jobid: 2 (Rule: FixChromName) 5 of 10 steps (50%) done Select jobs to execute... Execute 3 jobs... [Thu Aug 21 12:58:40 2025] localrule oxford2bed: input: results/example/example_imputed_ChromFixed, results/example/example_imputed_samples output: results/example/Imputed_example.bed, results/example/Imputed_example.bim, results/example/Imputed_example.fam log: results/example/logs/oxford2bed.log jobid: 1 reason: Missing output files: results/example/Imputed_example.bim, results/example/Imputed_example.bed, results/example/Imputed_example.fam; Input files updated by another job: results/example/example_imputed_ChromFixed, results/example/example_imputed_samples wildcards: dataout=results, sample=example resources: tmpdir=/rds/user/jhz22/hpc-work/work Activating conda environment: .snakemake/conda/f1f716d4caa09fcf1c22c007af0ac109 [Thu Aug 21 12:58:40 2025] localrule oxford2ped: input: results/example/example_imputed_ChromFixed, results/example/example_imputed_samples output: results/example/Imputed_example.map, results/example/Imputed_example.ped log: results/example/logs/oxford2ped.log jobid: 8 reason: Missing output files: results/example/Imputed_example.map, results/example/Imputed_example.ped; Input files updated by another job: results/example/example_imputed_ChromFixed, results/example/example_imputed_samples wildcards: dataout=results, sample=example resources: tmpdir=/rds/user/jhz22/hpc-work/work Activating conda environment: .snakemake/conda/f1f716d4caa09fcf1c22c007af0ac109 [Thu Aug 21 12:58:40 2025] localrule oxford2vcf: input: results/example/example_imputed_ChromFixed, results/example/example_imputed_samples output: results/example/Imputed_example.vcf log: results/example/logs/oxford2vcf.log jobid: 9 reason: Missing output files: results/example/Imputed_example.vcf; Input files updated by another job: results/example/example_imputed_ChromFixed, results/example/example_imputed_samples wildcards: dataout=results, sample=example resources: tmpdir=/rds/user/jhz22/hpc-work/work Activating conda environment: .snakemake/conda/f1f716d4caa09fcf1c22c007af0ac109 RuleException: CalledProcessError in file "/rds/project/rds-4o5vpvAowP0/software/MitoImpute/workflow/Snakefile", line 189: Command 'source /usr/local/Cluster-Apps/ceuadmin/miniforge3/bin/activate '/rds/project/rds-4o5vpvAowP0/software/MitoImpute/.snakemake/conda/f1f716d4caa09fcf1c22c007af0ac109'; set -euo pipefail; plink --gen results/example/example_imputed_ChromFixed --sample results/example/example_imputed_samples --hard-call-threshold 0.49 --keep-allele-order --output-chr 26 --recode --out results/example/Imputed_example &> results/example/logs/oxford2ped.log' returned non-zero exit status 3. [Thu Aug 21 12:58:41 2025] Error in rule oxford2ped: message: None jobid: 8 input: results/example/example_imputed_ChromFixed, results/example/example_imputed_samples output: results/example/Imputed_example.map, results/example/Imputed_example.ped log: results/example/logs/oxford2ped.log (check log file(s) for error details) conda-env: /rds/project/rds-4o5vpvAowP0/software/MitoImpute/.snakemake/conda/f1f716d4caa09fcf1c22c007af0ac109 shell: plink --gen results/example/example_imputed_ChromFixed --sample results/example/example_imputed_samples --hard-call-threshold 0.49 --keep-allele-order --output-chr 26 --recode --out results/example/Imputed_example &> results/example/logs/oxford2ped.log (command exited with non-zero exit code) RuleException: CalledProcessError in file "/rds/project/rds-4o5vpvAowP0/software/MitoImpute/workflow/Snakefile", line 208: Command 'source /usr/local/Cluster-Apps/ceuadmin/miniforge3/bin/activate '/rds/project/rds-4o5vpvAowP0/software/MitoImpute/.snakemake/conda/f1f716d4caa09fcf1c22c007af0ac109'; set -euo pipefail; plink --gen results/example/example_imputed_ChromFixed --sample results/example/example_imputed_samples --hard-call-threshold 0.49 --keep-allele-order --output-chr 26 --recode vcf --out results/example/Imputed_example &> results/example/logs/oxford2vcf.log' returned non-zero exit status 2. [Thu Aug 21 12:58:41 2025] Error in rule oxford2vcf: message: None jobid: 9 input: results/example/example_imputed_ChromFixed, results/example/example_imputed_samples output: results/example/Imputed_example.vcf log: results/example/logs/oxford2vcf.log (check log file(s) for error details) conda-env: /rds/project/rds-4o5vpvAowP0/software/MitoImpute/.snakemake/conda/f1f716d4caa09fcf1c22c007af0ac109 shell: plink --gen results/example/example_imputed_ChromFixed --sample results/example/example_imputed_samples --hard-call-threshold 0.49 --keep-allele-order --output-chr 26 --recode vcf --out results/example/Imputed_example &> results/example/logs/oxford2vcf.log (command exited with non-zero exit code) [Thu Aug 21 12:58:41 2025] Finished jobid: 1 (Rule: oxford2bed) 6 of 10 steps (60%) done Shutting down, this might take some time. Exiting because a job execution failed. Look below for error messages [Thu Aug 21 12:58:41 2025] Error in rule oxford2ped: message: None jobid: 8 input: results/example/example_imputed_ChromFixed, results/example/example_imputed_samples output: results/example/Imputed_example.map, results/example/Imputed_example.ped log: results/example/logs/oxford2ped.log (check log file(s) for error details) conda-env: /rds/project/rds-4o5vpvAowP0/software/MitoImpute/.snakemake/conda/f1f716d4caa09fcf1c22c007af0ac109 shell: plink --gen results/example/example_imputed_ChromFixed --sample results/example/example_imputed_samples --hard-call-threshold 0.49 --keep-allele-order --output-chr 26 --recode --out results/example/Imputed_example &> results/example/logs/oxford2ped.log (command exited with non-zero exit code) [Thu Aug 21 12:58:41 2025] Error in rule oxford2vcf: message: None jobid: 9 input: results/example/example_imputed_ChromFixed, results/example/example_imputed_samples output: results/example/Imputed_example.vcf log: results/example/logs/oxford2vcf.log (check log file(s) for error details) conda-env: /rds/project/rds-4o5vpvAowP0/software/MitoImpute/.snakemake/conda/f1f716d4caa09fcf1c22c007af0ac109 shell: plink --gen results/example/example_imputed_ChromFixed --sample results/example/example_imputed_samples --hard-call-threshold 0.49 --keep-allele-order --output-chr 26 --recode vcf --out results/example/Imputed_example &> results/example/logs/oxford2vcf.log (command exited with non-zero exit code) Complete log(s): /rds/project/rds-4o5vpvAowP0/software/MitoImpute/.snakemake/log/2025-08-21T125037.881663.snakemake.log WorkflowError: At least one job did not complete successfully.