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'.
Using shell: /usr/bin/bash
Provided cores: 3
Rules claiming more threads will be scaled down.
Job stats:
job           count
----------  -------
all               1
oxford2ped        1
oxford2vcf        1
plots             1
total             4

Select jobs to execute...
Execute 2 jobs...
[Thu Aug 21 15:57:14 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.ped, results/example/Imputed_example.map
    wildcards: dataout=results, sample=example
    resources: tmpdir=/rds/user/jhz22/hpc-work/work
Activating conda environment: .snakemake/conda/f1f716d4caa09fcf1c22c007af0ac109
[Thu Aug 21 15:57:15 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
    wildcards: dataout=results, sample=example
    resources: tmpdir=/rds/user/jhz22/hpc-work/work
Activating conda environment: .snakemake/conda/f1f716d4caa09fcf1c22c007af0ac109
[Thu Aug 21 15:57:25 2025]
Finished jobid: 8 (Rule: oxford2ped)
1 of 4 steps (25%) done
Select jobs to execute...
Execute 1 jobs...
[Thu Aug 21 15:57:25 2025]
localrule plots:
    input: results/example/example_typedOnly.map, results/example/example_typedOnly.ped, results/example/Imputed_example.map, results/example/Imputed_example.ped, results/example/example_imputed_info
    output: results/example/stats/example_Info.png, results/example/stats/example_InfoHiMC.png, results/example/stats/example_Haplogroups.txt, results/example/stats/example_HaplogroupMatch.png
    log: results/example/logs/plots.log
    jobid: 10
    reason: Missing output files: results/example/stats/example_Haplogroups.txt, results/example/stats/example_HaplogroupMatch.png, results/example/stats/example_InfoHiMC.png, results/example/stats/example_Info.png; Input files updated by another job: results/example/Imputed_example.ped, results/example/Imputed_example.map
    wildcards: dataout=results, sample=example
    resources: tmpdir=/rds/user/jhz22/hpc-work/work
[Thu Aug 21 15:57:25 2025]
Finished jobid: 9 (Rule: oxford2vcf)
2 of 4 steps (50%) done
Activating conda environment: .snakemake/conda/affd7974118e8caa2383ed3025b8c69b_
[Thu Aug 21 15:59:16 2025]
Finished jobid: 10 (Rule: plots)
3 of 4 steps (75%) done
Select jobs to execute...
Execute 1 jobs...
[Thu Aug 21 15:59:16 2025]
localrule all:
    input: results/example/Imputed_example.bed, results/example/Imputed_example.bim, results/example/Imputed_example.fam, results/example/Imputed_example.map, results/example/Imputed_example.ped, results/example/Imputed_example.vcf, results/example/stats/example_Info.png, results/example/stats/example_InfoHiMC.png, results/example/stats/example_Haplogroups.txt, results/example/stats/example_HaplogroupMatch.png
    jobid: 0
    reason: Input files updated by another job: results/example/Imputed_example.vcf, results/example/stats/example_Info.png, results/example/stats/example_Haplogroups.txt, results/example/stats/example_HaplogroupMatch.png, results/example/Imputed_example.ped, results/example/stats/example_InfoHiMC.png, results/example/Imputed_example.map
    resources: tmpdir=/rds/user/jhz22/hpc-work/work
[Thu Aug 21 15:59:16 2025]
Finished jobid: 0 (Rule: all)
4 of 4 steps (100%) done
Complete log(s): /rds/project/rds-4o5vpvAowP0/software/MitoImpute/.snakemake/log/2025-08-21T155619.469952.snakemake.log