diff --git a/.github/workflows/run_quick_tests.yaml b/.github/workflows/run_quick_tests.yaml index 190c359..849024f 100644 --- a/.github/workflows/run_quick_tests.yaml +++ b/.github/workflows/run_quick_tests.yaml @@ -2,25 +2,25 @@ name: Run quick tests of pipeline on: pull_request: - types: [closed] branches: - master workflow_dispatch: jobs: run-tests: - if: github.event.pull_request.merged == true || github.event_name == 'workflow_dispatch' runs-on: ubuntu-latest + container: + image: rocker/r-ver:4.1.0 + options: --privileged steps: - name: Checkout repository uses: actions/checkout@v3 - - name: Set up R - uses: r-lib/actions/setup-r@v2 - - - name: Setup singularity + - name: Setup Singularity uses: eWaterCycle/setup-singularity@v7 + with: + singularity-version: 3.8.3 - name: Download Singularity container run: | @@ -29,28 +29,25 @@ jobs: - name: Set environment variables run: | echo "SIF_FILE=$GITHUB_WORKSPACE/genopred_pipeline_latest.sif" >> $GITHUB_ENV - echo "BRANCH_NAME=${GITHUB_REF#refs/heads/}" >> $GITHUB_ENV - + if [ "${{ github.event_name }}" = "pull_request" ]; then + echo "BRANCH_NAME=${{ github.head_ref }}" >> $GITHUB_ENV + else + echo "BRANCH_NAME=${{ github.ref_name }}" >> $GITHUB_ENV + fi + - name: Install R dependencies run: | Rscript -e 'install.packages("testthat", repos="https://cran.rstudio.com/")' Rscript -e 'install.packages("data.table", repos="https://cran.rstudio.com/")' + Rscript -e 'install.packages("R.utils", repos="https://cran.rstudio.com/")' - name: Run tests run: | - mkdir -p test_results - Rscript -e "testthat::test_dir('pipeline/tests/testthat', reporter = 'junit')" > test_results/results.xml + Rscript -e "testthat::test_dir('pipeline/tests/testthat')" env: SIF_FILE: ${{ env.SIF_FILE }} BRANCH_NAME: ${{ env.BRANCH_NAME }} - - name: Upload test results - if: always() - uses: actions/upload-artifact@v3 - with: - name: test-results - path: test_results/results.xml - - name: Setup tmate session if: ${{ failure() }} uses: mxschmitt/action-tmate@v3 diff --git a/pipeline/misc/dev/test_data/output/example_plink2/ancestry/example_plink2.Ancestry.log b/pipeline/misc/dev/test_data/output/example_plink2/ancestry/example_plink2.Ancestry.log index 2c8eb05..95d943c 100644 --- a/pipeline/misc/dev/test_data/output/example_plink2/ancestry/example_plink2.Ancestry.log +++ b/pipeline/misc/dev/test_data/output/example_plink2/ancestry/example_plink2.Ancestry.log @@ -3,7 +3,7 @@ # For questions contact Oliver Pain (oliver.pain@kcl.ac.uk) ################################################################# # Repository: GenoPred -# Version (tag): v2.2.2-95-g19dbe57 +# Version (tag): v2.2.2-102-g0438efa --------------- Parameter Value target_plink_chr misc/dev/test_data/output/example_plink2/geno/example_plink2.ref.chr @@ -23,7 +23,7 @@ help FALSE out_dir misc/dev/test_data/output/example_plink2/ancestry/ --------------- -Analysis started at 2024-07-25 09:40:29 +Analysis started at 2024-07-25 15:07:05 Lowering prob_thresh parameter to 0.5 for testing. Target sample size is <100 so only checking genotype missingness. 587 variants match between target and reference after QC. @@ -47,5 +47,5 @@ N per group based on model: MID 0 Unassigned 2 ---------- -Analysis finished at 2024-07-25 09:40:44 -Analysis duration was 15.33 secs +Analysis finished at 2024-07-25 15:07:19 +Analysis duration was 14.27 secs diff --git a/pipeline/misc/dev/test_data/output/example_plink2/ancestry/example_plink2.Ancestry.pc_plot.png b/pipeline/misc/dev/test_data/output/example_plink2/ancestry/example_plink2.Ancestry.pc_plot.png index 058590b..ed1cb6c 100644 Binary files a/pipeline/misc/dev/test_data/output/example_plink2/ancestry/example_plink2.Ancestry.pc_plot.png and b/pipeline/misc/dev/test_data/output/example_plink2/ancestry/example_plink2.Ancestry.pc_plot.png differ diff --git a/pipeline/misc/dev/test_data/output/example_plink2/geno/example_plink2.ref.chr22.format_target.log b/pipeline/misc/dev/test_data/output/example_plink2/geno/example_plink2.ref.chr22.format_target.log index b6d8787..1731490 100644 --- a/pipeline/misc/dev/test_data/output/example_plink2/geno/example_plink2.ref.chr22.format_target.log +++ b/pipeline/misc/dev/test_data/output/example_plink2/geno/example_plink2.ref.chr22.format_target.log @@ -3,7 +3,7 @@ # For questions contact Oliver Pain (oliver.pain@kcl.ac.uk) ################################################################# # Repository: GenoPred -# Version (tag): v2.2.2-95-g19dbe57 +# Version (tag): v2.2.2-102-g0438efa --------------- Parameter Value target misc/dev/test_data/target/example.chr22 @@ -15,7 +15,7 @@ help FALSE out_dir misc/dev/test_data/output/example_plink2/geno/ --------------- -Analysis started at 2024-07-25 09:40:19 +Analysis started at 2024-07-25 15:07:00 Reading in reference SNP data. Reference data contains 1000 variants. Reading in target SNP data. @@ -26,5 +26,5 @@ GRCh38 match: 0% Target contains 1000 reference variants. Removing 0 duplicate variants - May have IUPAC NA. Inserting missing reference variants. -Analysis finished at 2024-07-25 09:40:23 -Analysis duration was 4.25 secs +Analysis finished at 2024-07-25 15:07:01 +Analysis duration was 0.7 secs diff --git a/pipeline/misc/dev/test_data/output/example_plink2/geno/example_plink2.ref.chr22.log b/pipeline/misc/dev/test_data/output/example_plink2/geno/example_plink2.ref.chr22.log index 254dc23..be6ffba 100644 --- a/pipeline/misc/dev/test_data/output/example_plink2/geno/example_plink2.ref.chr22.log +++ b/pipeline/misc/dev/test_data/output/example_plink2/geno/example_plink2.ref.chr22.log @@ -1,24 +1,24 @@ -PLINK v2.00a5LM 64-bit Intel (23 Sep 2023) +PLINK v2.00a5.12LM 64-bit Intel (25 Jun 2024) Options in effect: - --bfile /scratch/prj/oliverpainfel/tmp/RtmpClbFKL/ref_targ + --bfile /scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/ref_targ --make-pgen --memory 5000 --out misc/dev/test_data/output/example_plink2/geno/example_plink2.ref.chr22 - --remove /scratch/prj/oliverpainfel/tmp/RtmpClbFKL/REF.psam + --remove /scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/REF.psam --threads 1 Hostname: erc-hpc-comp179 -Working directory: /scratch/prj/oliverpainfel/Software/MyGit/GenoPred/pipeline -Start time: Thu Jul 25 09:40:23 2024 +Working directory: /tools/GenoPred/pipeline +Start time: Thu Jul 25 15:07:01 2024 -Random number seed: 1721896823 -1031702 MiB RAM detected, ~1018874 available; reserving 5000 MiB for main +Random number seed: 1721916421 +1031702 MiB RAM detected, ~1018552 available; reserving 5000 MiB for main workspace. Using 1 compute thread. 3325 samples (1573 females, 1752 males; 3325 founders) loaded from -/scratch/prj/oliverpainfel/tmp/RtmpClbFKL/ref_targ.fam. +/scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/ref_targ.fam. 1000 variants loaded from -/scratch/prj/oliverpainfel/tmp/RtmpClbFKL/ref_targ.bim. +/scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/ref_targ.bim. Note: No phenotype data present. --remove: 12 samples remaining. 12 samples (5 females, 7 males; 12 founders) remaining after main filters. @@ -32,4 +32,4 @@ Writing misc/dev/test_data/output/example_plink2/geno/example_plink2.ref.chr22.pgen ... done. -End time: Thu Jul 25 09:40:23 2024 +End time: Thu Jul 25 15:07:01 2024 diff --git a/pipeline/misc/dev/test_data/output/example_plink2/pcs/projected/AFR/example_plink2-AFR.log b/pipeline/misc/dev/test_data/output/example_plink2/pcs/projected/AFR/example_plink2-AFR.log index 05bc313..001539c 100644 --- a/pipeline/misc/dev/test_data/output/example_plink2/pcs/projected/AFR/example_plink2-AFR.log +++ b/pipeline/misc/dev/test_data/output/example_plink2/pcs/projected/AFR/example_plink2-AFR.log @@ -3,7 +3,7 @@ # For questions contact Oliver Pain (oliver.pain@kcl.ac.uk) ################################################################# # Repository: GenoPred -# Version (tag): v2.2.2-95-g19dbe57 +# Version (tag): v2.2.2-102-g0438efa --------------- Parameter Value target_plink_chr misc/dev/test_data/output/example_plink2/geno/example_plink2.ref.chr @@ -19,9 +19,9 @@ help FALSE output_dir misc/dev/test_data/output/example_plink2/pcs/projected/AFR/ --------------- -Analysis started at 2024-07-25 09:41:24 +Analysis started at 2024-07-25 15:07:20 Calculating polygenic scores in the target sample. Scaling target polygenic scores to the reference. Saved polygenic scores to: misc/dev/test_data/output/example_plink2/pcs/projected/AFR/example_plink2-AFR.profiles. -Analysis finished at 2024-07-25 09:41:25 -Analysis duration was 0.92 secs +Analysis finished at 2024-07-25 15:07:20 +Analysis duration was 0.22 secs diff --git a/pipeline/misc/dev/test_data/output/example_plink2/pcs/projected/CSA/example_plink2-CSA.log b/pipeline/misc/dev/test_data/output/example_plink2/pcs/projected/CSA/example_plink2-CSA.log index a50bbc3..e1b7f83 100644 --- a/pipeline/misc/dev/test_data/output/example_plink2/pcs/projected/CSA/example_plink2-CSA.log +++ b/pipeline/misc/dev/test_data/output/example_plink2/pcs/projected/CSA/example_plink2-CSA.log @@ -3,7 +3,7 @@ # For questions contact Oliver Pain (oliver.pain@kcl.ac.uk) ################################################################# # Repository: GenoPred -# Version (tag): v2.2.2-95-g19dbe57 +# Version (tag): v2.2.2-102-g0438efa --------------- Parameter Value target_plink_chr misc/dev/test_data/output/example_plink2/geno/example_plink2.ref.chr @@ -19,9 +19,9 @@ help FALSE output_dir misc/dev/test_data/output/example_plink2/pcs/projected/CSA/ --------------- -Analysis started at 2024-07-25 09:41:14 +Analysis started at 2024-07-25 15:07:22 Calculating polygenic scores in the target sample. Scaling target polygenic scores to the reference. Saved polygenic scores to: misc/dev/test_data/output/example_plink2/pcs/projected/CSA/example_plink2-CSA.profiles. -Analysis finished at 2024-07-25 09:41:16 -Analysis duration was 1.51 secs +Analysis finished at 2024-07-25 15:07:22 +Analysis duration was 0.22 secs diff --git a/pipeline/misc/dev/test_data/output/example_plink2/pcs/projected/EAS/example_plink2-EAS.log b/pipeline/misc/dev/test_data/output/example_plink2/pcs/projected/EAS/example_plink2-EAS.log index fde6c88..f6d4ee3 100644 --- a/pipeline/misc/dev/test_data/output/example_plink2/pcs/projected/EAS/example_plink2-EAS.log +++ b/pipeline/misc/dev/test_data/output/example_plink2/pcs/projected/EAS/example_plink2-EAS.log @@ -3,7 +3,7 @@ # For questions contact Oliver Pain (oliver.pain@kcl.ac.uk) ################################################################# # Repository: GenoPred -# Version (tag): v2.2.2-95-g19dbe57 +# Version (tag): v2.2.2-102-g0438efa --------------- Parameter Value target_plink_chr misc/dev/test_data/output/example_plink2/geno/example_plink2.ref.chr @@ -19,9 +19,9 @@ help FALSE output_dir misc/dev/test_data/output/example_plink2/pcs/projected/EAS/ --------------- -Analysis started at 2024-07-25 09:41:07 +Analysis started at 2024-07-25 15:07:21 Calculating polygenic scores in the target sample. Scaling target polygenic scores to the reference. Saved polygenic scores to: misc/dev/test_data/output/example_plink2/pcs/projected/EAS/example_plink2-EAS.profiles. -Analysis finished at 2024-07-25 09:41:09 -Analysis duration was 2.18 secs +Analysis finished at 2024-07-25 15:07:22 +Analysis duration was 0.24 secs diff --git a/pipeline/misc/dev/test_data/output/example_plink2/pcs/projected/EUR/example_plink2-EUR.log b/pipeline/misc/dev/test_data/output/example_plink2/pcs/projected/EUR/example_plink2-EUR.log index 77f8e48..36df935 100644 --- a/pipeline/misc/dev/test_data/output/example_plink2/pcs/projected/EUR/example_plink2-EUR.log +++ b/pipeline/misc/dev/test_data/output/example_plink2/pcs/projected/EUR/example_plink2-EUR.log @@ -3,7 +3,7 @@ # For questions contact Oliver Pain (oliver.pain@kcl.ac.uk) ################################################################# # Repository: GenoPred -# Version (tag): v2.2.2-95-g19dbe57 +# Version (tag): v2.2.2-102-g0438efa --------------- Parameter Value target_plink_chr misc/dev/test_data/output/example_plink2/geno/example_plink2.ref.chr @@ -19,9 +19,9 @@ help FALSE output_dir misc/dev/test_data/output/example_plink2/pcs/projected/EUR/ --------------- -Analysis started at 2024-07-25 09:40:59 +Analysis started at 2024-07-25 15:07:21 Calculating polygenic scores in the target sample. Scaling target polygenic scores to the reference. Saved polygenic scores to: misc/dev/test_data/output/example_plink2/pcs/projected/EUR/example_plink2-EUR.profiles. -Analysis finished at 2024-07-25 09:41:01 -Analysis duration was 1.79 secs +Analysis finished at 2024-07-25 15:07:21 +Analysis duration was 0.24 secs diff --git a/pipeline/misc/dev/test_data/output/example_plink2/pgs/AFR.log b/pipeline/misc/dev/test_data/output/example_plink2/pgs/AFR.log index 463159b..e105b26 100644 --- a/pipeline/misc/dev/test_data/output/example_plink2/pgs/AFR.log +++ b/pipeline/misc/dev/test_data/output/example_plink2/pgs/AFR.log @@ -3,7 +3,7 @@ # For questions contact Oliver Pain (oliver.pain@kcl.ac.uk) ################################################################# # Repository: GenoPred -# Version (tag): v2.2.2-95-g19dbe57 +# Version (tag): v2.2.2-102-g0438efa --------------- Parameter Value config misc/dev/test_data/config/config.yaml @@ -16,7 +16,7 @@ help FALSE output_dir misc/dev/test_data/output/example_plink2/pgs/AFR --------------- -Analysis started at 2024-07-25 11:37:16 +Analysis started at 2024-07-25 15:07:25 Processing 3 score files. Aggregating score files in 1 batches. Aggregating batched score files. @@ -24,5 +24,5 @@ Reading in scale files. Calculating polygenic scores in the target sample. Scaling target polygenic scores to the reference. Saved polygenic scores. -Analysis finished at 2024-07-25 11:37:16 -Analysis duration was 0.34 secs +Analysis finished at 2024-07-25 15:07:26 +Analysis duration was 0.35 secs diff --git a/pipeline/misc/dev/test_data/output/example_plink2/pgs/CSA.log b/pipeline/misc/dev/test_data/output/example_plink2/pgs/CSA.log index 6c4f22e..136923a 100644 --- a/pipeline/misc/dev/test_data/output/example_plink2/pgs/CSA.log +++ b/pipeline/misc/dev/test_data/output/example_plink2/pgs/CSA.log @@ -3,7 +3,7 @@ # For questions contact Oliver Pain (oliver.pain@kcl.ac.uk) ################################################################# # Repository: GenoPred -# Version (tag): v2.2.2-95-g19dbe57 +# Version (tag): v2.2.2-102-g0438efa --------------- Parameter Value config misc/dev/test_data/config/config.yaml @@ -16,7 +16,7 @@ help FALSE output_dir misc/dev/test_data/output/example_plink2/pgs/CSA --------------- -Analysis started at 2024-07-25 11:37:17 +Analysis started at 2024-07-25 15:07:26 Processing 3 score files. Aggregating score files in 1 batches. Aggregating batched score files. @@ -24,5 +24,5 @@ Reading in scale files. Calculating polygenic scores in the target sample. Scaling target polygenic scores to the reference. Saved polygenic scores. -Analysis finished at 2024-07-25 11:37:19 -Analysis duration was 1.99 secs +Analysis finished at 2024-07-25 15:07:26 +Analysis duration was 0.34 secs diff --git a/pipeline/misc/dev/test_data/output/example_plink2/pgs/EAS.log b/pipeline/misc/dev/test_data/output/example_plink2/pgs/EAS.log index 517138b..d1a4426 100644 --- a/pipeline/misc/dev/test_data/output/example_plink2/pgs/EAS.log +++ b/pipeline/misc/dev/test_data/output/example_plink2/pgs/EAS.log @@ -3,7 +3,7 @@ # For questions contact Oliver Pain (oliver.pain@kcl.ac.uk) ################################################################# # Repository: GenoPred -# Version (tag): v2.2.2-95-g19dbe57 +# Version (tag): v2.2.2-102-g0438efa --------------- Parameter Value config misc/dev/test_data/config/config.yaml @@ -16,7 +16,7 @@ help FALSE output_dir misc/dev/test_data/output/example_plink2/pgs/EAS --------------- -Analysis started at 2024-07-25 11:37:15 +Analysis started at 2024-07-25 15:07:24 Processing 3 score files. Aggregating score files in 1 batches. Aggregating batched score files. @@ -24,5 +24,5 @@ Reading in scale files. Calculating polygenic scores in the target sample. Scaling target polygenic scores to the reference. Saved polygenic scores. -Analysis finished at 2024-07-25 11:37:15 -Analysis duration was 0.39 secs +Analysis finished at 2024-07-25 15:07:25 +Analysis duration was 0.32 secs diff --git a/pipeline/misc/dev/test_data/output/example_plink2/pgs/EUR.log b/pipeline/misc/dev/test_data/output/example_plink2/pgs/EUR.log index c0116d8..a110897 100644 --- a/pipeline/misc/dev/test_data/output/example_plink2/pgs/EUR.log +++ b/pipeline/misc/dev/test_data/output/example_plink2/pgs/EUR.log @@ -3,7 +3,7 @@ # For questions contact Oliver Pain (oliver.pain@kcl.ac.uk) ################################################################# # Repository: GenoPred -# Version (tag): v2.2.2-95-g19dbe57 +# Version (tag): v2.2.2-102-g0438efa --------------- Parameter Value config misc/dev/test_data/config/config.yaml @@ -16,7 +16,7 @@ help FALSE output_dir misc/dev/test_data/output/example_plink2/pgs/EUR --------------- -Analysis started at 2024-07-25 11:37:14 +Analysis started at 2024-07-25 15:07:24 Processing 3 score files. Aggregating score files in 1 batches. Aggregating batched score files. @@ -24,5 +24,5 @@ Reading in scale files. Calculating polygenic scores in the target sample. Scaling target polygenic scores to the reference. Saved polygenic scores. -Analysis finished at 2024-07-25 11:37:15 -Analysis duration was 0.48 secs +Analysis finished at 2024-07-25 15:07:24 +Analysis duration was 0.35 secs diff --git a/pipeline/misc/dev/test_data/output/example_plink2/reports/example_plink2-report.html b/pipeline/misc/dev/test_data/output/example_plink2/reports/example_plink2-report.html index c4aef3f..4f2ec9f 100644 --- a/pipeline/misc/dev/test_data/output/example_plink2/reports/example_plink2-report.html +++ b/pipeline/misc/dev/test_data/output/example_plink2/reports/example_plink2-report.html @@ -3978,14 +3978,14 @@

Ancestry

reference population with a probability >50%.
  • The number of individuals assigned to each population were:
    • -
    - +
    +


    Show principal component plots -

    Target +

    Target Principal Component Scores Compared to Reference Populations.

    Note. Black circles indicate target sample @@ -4003,14 +4003,14 @@

    Polygenic Scores

    GWAS summary statistics

    -
    - +
    +

    Score files

    -
    - +
    +

    Note. The Pass column indicates whether a sufficient number of variants within the score file were present in the reference data.

    @@ -4044,7 +4044,7 @@

    external

    -

    This report was created using GenoPred (v2.2.2-95-g19dbe57).

    +

    This report was created using GenoPred (v2.2.2-102-g0438efa).

    diff --git a/pipeline/misc/dev/test_data/output/example_plink2/reports/individual/example_plink2-4_EAS.4_EAS-report.html b/pipeline/misc/dev/test_data/output/example_plink2/reports/individual/example_plink2-4_EAS.4_EAS-report.html index 3e9326f..13b61d1 100644 --- a/pipeline/misc/dev/test_data/output/example_plink2/reports/individual/example_plink2-4_EAS.4_EAS-report.html +++ b/pipeline/misc/dev/test_data/output/example_plink2/reports/individual/example_plink2-4_EAS.4_EAS-report.html @@ -4000,14 +4000,14 @@

    Polygenic Scores

    GWAS summary statistics

    -
    - +
    +

    Score files

    -
    - +
    +

    Note. The Pass column indicates whether a sufficient number of variants within the score file were present in the reference data.

    @@ -4114,7 +4114,7 @@

    Method: lassosum

    GWAS: Body Mass Index

    -

    +

    • Your PGS Z-score for Body Mass IndexBody Mass Index is 0.994 @@ -4229,7 +4229,7 @@

      Method: pT+clump

      GWAS: Body Mass Index

      -

      +

      • Your PGS Z-score for Body Mass IndexBody Mass Index is 1.486 @@ -4344,7 +4344,7 @@

        Method: External

        GWAS: Height Yengo EUR

        -

        +

        • Your PGS Z-score for Height Yengo EUR is -0.711 which is higher than @@ -4357,7 +4357,7 @@

          GWAS: Height Yengo EUR

          -

          This report was created using GenoPred (v2.2.2-95-g19dbe57).

          +

          This report was created using GenoPred (v2.2.2-102-g0438efa).

      diff --git a/pipeline/misc/dev/test_data/output/reference/benchmarks/ancestry_inference_i-example_plink2.txt b/pipeline/misc/dev/test_data/output/reference/benchmarks/ancestry_inference_i-example_plink2.txt index c6a1582..2c8b28b 100644 --- a/pipeline/misc/dev/test_data/output/reference/benchmarks/ancestry_inference_i-example_plink2.txt +++ b/pipeline/misc/dev/test_data/output/reference/benchmarks/ancestry_inference_i-example_plink2.txt @@ -1,2 +1,2 @@ s h:m:s max_rss max_vms max_uss max_pss io_in io_out mean_load cpu_time -17.9874 0:00:17 441.39 4642.98 437.00 437.74 0.00 1.20 64.70 11.98 +14.6503 0:00:14 451.30 516539.48 447.39 449.39 0.00 1.07 80.62 12.61 diff --git a/pipeline/misc/dev/test_data/output/reference/benchmarks/ancestry_reporter-example_plink2.txt b/pipeline/misc/dev/test_data/output/reference/benchmarks/ancestry_reporter-example_plink2.txt index 19d45a2..14f84fd 100644 --- a/pipeline/misc/dev/test_data/output/reference/benchmarks/ancestry_reporter-example_plink2.txt +++ b/pipeline/misc/dev/test_data/output/reference/benchmarks/ancestry_reporter-example_plink2.txt @@ -1,2 +1,2 @@ s h:m:s max_rss max_vms max_uss max_pss io_in io_out mean_load cpu_time -0.3615 0:00:00 3.00 9.88 0.04 0.58 0.00 0.00 0.00 0.00 +0.3222 0:00:00 0 2.03 0.12 0.27 0.00 0.00 0.00 0.00 diff --git a/pipeline/misc/dev/test_data/output/reference/benchmarks/format_target_i-example_plink2-22.txt b/pipeline/misc/dev/test_data/output/reference/benchmarks/format_target_i-example_plink2-22.txt index 94a0f34..ccfc935 100644 --- a/pipeline/misc/dev/test_data/output/reference/benchmarks/format_target_i-example_plink2-22.txt +++ b/pipeline/misc/dev/test_data/output/reference/benchmarks/format_target_i-example_plink2-22.txt @@ -1,2 +1,2 @@ s h:m:s max_rss max_vms max_uss max_pss io_in io_out mean_load cpu_time -4.6663 0:00:04 110.76 5348.30 103.86 104.58 0.00 3.69 4.52 0.53 +1.0635 0:00:01 70.83 158.56 67.31 69.17 0.00 0.00 0.00 0.31 diff --git a/pipeline/misc/dev/test_data/output/reference/benchmarks/indiv_report_i-example_plink2-4_EAS.4_EAS.txt b/pipeline/misc/dev/test_data/output/reference/benchmarks/indiv_report_i-example_plink2-4_EAS.4_EAS.txt index 1b74e85..cccdf33 100644 --- a/pipeline/misc/dev/test_data/output/reference/benchmarks/indiv_report_i-example_plink2-4_EAS.4_EAS.txt +++ b/pipeline/misc/dev/test_data/output/reference/benchmarks/indiv_report_i-example_plink2-4_EAS.4_EAS.txt @@ -1,2 +1,2 @@ s h:m:s max_rss max_vms max_uss max_pss io_in io_out mean_load cpu_time -5.0812 0:00:05 367.09 858.32 360.86 361.77 0.00 1.75 78.74 4.30 +5.4381 0:00:05 375.84 769.37 372.47 374.81 0.00 0.19 72.60 4.23 diff --git a/pipeline/misc/dev/test_data/output/reference/benchmarks/pc_projection_i-example_plink2-AFR.txt b/pipeline/misc/dev/test_data/output/reference/benchmarks/pc_projection_i-example_plink2-AFR.txt index 3f87930..8444f89 100644 --- a/pipeline/misc/dev/test_data/output/reference/benchmarks/pc_projection_i-example_plink2-AFR.txt +++ b/pipeline/misc/dev/test_data/output/reference/benchmarks/pc_projection_i-example_plink2-AFR.txt @@ -1,2 +1,2 @@ s h:m:s max_rss max_vms max_uss max_pss io_in io_out mean_load cpu_time -1.3357 0:00:01 70.16 241.25 64.66 65.35 0.00 0.05 8.31 0.31 +0.5640 0:00:00 72.84 227.62 67.83 70.07 0.00 0.04 0.00 0.28 diff --git a/pipeline/misc/dev/test_data/output/reference/benchmarks/pc_projection_i-example_plink2-CSA.txt b/pipeline/misc/dev/test_data/output/reference/benchmarks/pc_projection_i-example_plink2-CSA.txt index a9fb653..7537e26 100644 --- a/pipeline/misc/dev/test_data/output/reference/benchmarks/pc_projection_i-example_plink2-CSA.txt +++ b/pipeline/misc/dev/test_data/output/reference/benchmarks/pc_projection_i-example_plink2-CSA.txt @@ -1,2 +1,2 @@ s h:m:s max_rss max_vms max_uss max_pss io_in io_out mean_load cpu_time -2.0147 0:00:02 70.16 241.26 64.70 65.41 0.00 0.04 5.55 0.31 +0.5473 0:00:00 2.00 4.36 0.08 1.40 0.00 0.00 0.00 0.00 diff --git a/pipeline/misc/dev/test_data/output/reference/benchmarks/pc_projection_i-example_plink2-EAS.txt b/pipeline/misc/dev/test_data/output/reference/benchmarks/pc_projection_i-example_plink2-EAS.txt index 00f090e..e28dcf0 100644 --- a/pipeline/misc/dev/test_data/output/reference/benchmarks/pc_projection_i-example_plink2-EAS.txt +++ b/pipeline/misc/dev/test_data/output/reference/benchmarks/pc_projection_i-example_plink2-EAS.txt @@ -1,2 +1,2 @@ s h:m:s max_rss max_vms max_uss max_pss io_in io_out mean_load cpu_time -2.7472 0:00:02 69.16 259.61 63.95 64.67 0.00 0.03 3.27 0.29 +0.5695 0:00:00 70.84 222.18 67.38 69.07 0.00 0.03 0.00 0.28 diff --git a/pipeline/misc/dev/test_data/output/reference/benchmarks/pc_projection_i-example_plink2-EUR.txt b/pipeline/misc/dev/test_data/output/reference/benchmarks/pc_projection_i-example_plink2-EUR.txt index a47954c..49a2a57 100644 --- a/pipeline/misc/dev/test_data/output/reference/benchmarks/pc_projection_i-example_plink2-EUR.txt +++ b/pipeline/misc/dev/test_data/output/reference/benchmarks/pc_projection_i-example_plink2-EUR.txt @@ -1,2 +1,2 @@ s h:m:s max_rss max_vms max_uss max_pss io_in io_out mean_load cpu_time -2.6030 0:00:02 72.16 260.31 65.09 65.89 0.00 0.04 4.14 0.31 +0.5673 0:00:00 70.52 222.23 67.42 69.29 0.00 0.03 0.00 0.28 diff --git a/pipeline/misc/dev/test_data/output/reference/benchmarks/prep_pgs_lassosum_i-BODY04.txt b/pipeline/misc/dev/test_data/output/reference/benchmarks/prep_pgs_lassosum_i-BODY04.txt index ce57008..680595d 100644 --- a/pipeline/misc/dev/test_data/output/reference/benchmarks/prep_pgs_lassosum_i-BODY04.txt +++ b/pipeline/misc/dev/test_data/output/reference/benchmarks/prep_pgs_lassosum_i-BODY04.txt @@ -1,2 +1,2 @@ s h:m:s max_rss max_vms max_uss max_pss io_in io_out mean_load cpu_time -27.3731 0:00:27 253.16 568.40 240.51 244.92 0.00 0.57 4.14 1.34 +3.1643 0:00:03 264.84 550.32 250.21 257.22 0.00 0.26 28.43 1.22 diff --git a/pipeline/misc/dev/test_data/output/reference/benchmarks/prep_pgs_ptclump_i-BODY04.txt b/pipeline/misc/dev/test_data/output/reference/benchmarks/prep_pgs_ptclump_i-BODY04.txt index 2bc3794..54bb1c1 100644 --- a/pipeline/misc/dev/test_data/output/reference/benchmarks/prep_pgs_ptclump_i-BODY04.txt +++ b/pipeline/misc/dev/test_data/output/reference/benchmarks/prep_pgs_ptclump_i-BODY04.txt @@ -1,2 +1,2 @@ s h:m:s max_rss max_vms max_uss max_pss io_in io_out mean_load cpu_time -0.8348 0:00:00 68.16 259.14 63.45 63.98 0.00 0.07 0.00 0.28 +1.0572 0:00:01 69.93 213.49 66.80 68.63 0.00 0.06 0.00 0.28 diff --git a/pipeline/misc/dev/test_data/output/reference/benchmarks/sample_report_i-example_plink2.txt b/pipeline/misc/dev/test_data/output/reference/benchmarks/sample_report_i-example_plink2.txt index 76dd0ef..28ab6d1 100644 --- a/pipeline/misc/dev/test_data/output/reference/benchmarks/sample_report_i-example_plink2.txt +++ b/pipeline/misc/dev/test_data/output/reference/benchmarks/sample_report_i-example_plink2.txt @@ -1,2 +1,2 @@ s h:m:s max_rss max_vms max_uss max_pss io_in io_out mean_load cpu_time -2.5578 0:00:02 189.13 480.65 184.38 185.05 0.00 0.21 60.74 1.85 +3.3662 0:00:03 283.84 1049383.44 278.54 281.12 0.00 0.18 47.47 1.86 diff --git a/pipeline/misc/dev/test_data/output/reference/benchmarks/score_reporter.txt b/pipeline/misc/dev/test_data/output/reference/benchmarks/score_reporter.txt index 1a3f736..23e08c5 100644 --- a/pipeline/misc/dev/test_data/output/reference/benchmarks/score_reporter.txt +++ b/pipeline/misc/dev/test_data/output/reference/benchmarks/score_reporter.txt @@ -1,2 +1,2 @@ s h:m:s max_rss max_vms max_uss max_pss io_in io_out mean_load cpu_time -0.4543 0:00:00 3.00 9.88 0.13 0.45 0.00 0.00 0.00 0.00 +0.5902 0:00:00 67.83 211.89 64.77 66.63 0.00 0.00 0.00 0.20 diff --git a/pipeline/misc/dev/test_data/output/reference/benchmarks/sumstat_prep_i-BODY04.txt b/pipeline/misc/dev/test_data/output/reference/benchmarks/sumstat_prep_i-BODY04.txt index 592eb19..3d5d0fd 100644 --- a/pipeline/misc/dev/test_data/output/reference/benchmarks/sumstat_prep_i-BODY04.txt +++ b/pipeline/misc/dev/test_data/output/reference/benchmarks/sumstat_prep_i-BODY04.txt @@ -1,2 +1,2 @@ s h:m:s max_rss max_vms max_uss max_pss io_in io_out mean_load cpu_time -2.1025 0:00:02 65.16 173.61 60.70 61.39 0.00 0.01 7.50 0.21 +0.6514 0:00:00 66.22 146.18 62.94 64.84 0.00 0.00 0.00 0.18 diff --git a/pipeline/misc/dev/test_data/output/reference/benchmarks/target_pgs_i-example_plink2-AFR.txt b/pipeline/misc/dev/test_data/output/reference/benchmarks/target_pgs_i-example_plink2-AFR.txt index e85f98a..699198b 100644 --- a/pipeline/misc/dev/test_data/output/reference/benchmarks/target_pgs_i-example_plink2-AFR.txt +++ b/pipeline/misc/dev/test_data/output/reference/benchmarks/target_pgs_i-example_plink2-AFR.txt @@ -1,2 +1,2 @@ s h:m:s max_rss max_vms max_uss max_pss io_in io_out mean_load cpu_time -0.7081 0:00:00 68.79 240.32 63.73 64.31 0.00 0.02 0.00 0.27 +0.7000 0:00:00 70.11 213.58 66.72 68.45 0.00 0.54 0.00 0.25 diff --git a/pipeline/misc/dev/test_data/output/reference/benchmarks/target_pgs_i-example_plink2-CSA.txt b/pipeline/misc/dev/test_data/output/reference/benchmarks/target_pgs_i-example_plink2-CSA.txt index f100399..e4759ad 100644 --- a/pipeline/misc/dev/test_data/output/reference/benchmarks/target_pgs_i-example_plink2-CSA.txt +++ b/pipeline/misc/dev/test_data/output/reference/benchmarks/target_pgs_i-example_plink2-CSA.txt @@ -1,2 +1,2 @@ s h:m:s max_rss max_vms max_uss max_pss io_in io_out mean_load cpu_time -2.3634 0:00:02 71.16 251.67 64.50 65.18 0.00 0.84 2.04 0.32 +0.6770 0:00:00 69.30 213.58 66.81 68.48 0.00 0.27 0.00 0.25 diff --git a/pipeline/misc/dev/test_data/output/reference/benchmarks/target_pgs_i-example_plink2-EAS.txt b/pipeline/misc/dev/test_data/output/reference/benchmarks/target_pgs_i-example_plink2-EAS.txt index f3e5101..d7d0b7d 100644 --- a/pipeline/misc/dev/test_data/output/reference/benchmarks/target_pgs_i-example_plink2-EAS.txt +++ b/pipeline/misc/dev/test_data/output/reference/benchmarks/target_pgs_i-example_plink2-EAS.txt @@ -1,2 +1,2 @@ s h:m:s max_rss max_vms max_uss max_pss io_in io_out mean_load cpu_time -0.7482 0:00:00 69.79 243.15 63.85 64.49 0.00 0.02 0.00 0.27 +0.7203 0:00:00 69.91 213.58 66.53 68.36 0.00 0.00 0.00 0.23 diff --git a/pipeline/misc/dev/test_data/output/reference/benchmarks/target_pgs_i-example_plink2-EUR.txt b/pipeline/misc/dev/test_data/output/reference/benchmarks/target_pgs_i-example_plink2-EUR.txt index c029185..426cf09 100644 --- a/pipeline/misc/dev/test_data/output/reference/benchmarks/target_pgs_i-example_plink2-EUR.txt +++ b/pipeline/misc/dev/test_data/output/reference/benchmarks/target_pgs_i-example_plink2-EUR.txt @@ -1,2 +1,2 @@ s h:m:s max_rss max_vms max_uss max_pss io_in io_out mean_load cpu_time -0.8555 0:00:00 67.16 233.05 62.78 63.33 0.00 0.00 0.00 0.22 +0.6792 0:00:00 72.84 224.52 67.43 69.73 0.00 0.27 0.00 0.25 diff --git a/pipeline/misc/dev/test_data/output/reference/gwas_sumstat/BODY04/BODY04-cleaned.log b/pipeline/misc/dev/test_data/output/reference/gwas_sumstat/BODY04/BODY04-cleaned.log index 7ccdc65..659160b 100644 --- a/pipeline/misc/dev/test_data/output/reference/gwas_sumstat/BODY04/BODY04-cleaned.log +++ b/pipeline/misc/dev/test_data/output/reference/gwas_sumstat/BODY04/BODY04-cleaned.log @@ -16,7 +16,7 @@ test chr22 help FALSE --------------- -Analysis started at 2024-07-25 09:40:25 +Analysis started at 2024-07-25 15:07:01 Reading in sumstats. GWAS contains 885 variants. --------------- @@ -42,5 +42,5 @@ After removal of SNPs with duplicate IDs, 871 variants remain. After removal of SNPs with N > 334358.59618899 or < 126741.40381101, 841 variants remain. Genomic control was not detected. After removal of SNPs with SE == 0, 841 variants remain. -Analysis finished at 2024-07-25 09:40:26 -Analysis duration was 1.42secs +Analysis finished at 2024-07-25 15:07:02 +Analysis duration was 0.2secs diff --git a/pipeline/misc/dev/test_data/output/reference/logs/ancestry_inference_i-example_plink2.log b/pipeline/misc/dev/test_data/output/reference/logs/ancestry_inference_i-example_plink2.log index a391634..4b02a32 100644 --- a/pipeline/misc/dev/test_data/output/reference/logs/ancestry_inference_i-example_plink2.log +++ b/pipeline/misc/dev/test_data/output/reference/logs/ancestry_inference_i-example_plink2.log @@ -1,3 +1,10 @@ +During startup - Warning messages: +1: Setting LC_COLLATE failed, using "C" +2: Setting LC_TIME failed, using "C" +3: Setting LC_MESSAGES failed, using "C" +4: Setting LC_MONETARY failed, using "C" +5: Setting LC_PAPER failed, using "C" +6: Setting LC_MEASUREMENT failed, using "C" Loading required package: ggplot2 Loading required package: lattice Type 'citation("pROC")' for a citation. @@ -64,19 +71,19 @@ The following object is masked from ‘package:pROC’: lines.roc -PLINK v2.00a5LM 64-bit Intel (23 Sep 2023) www.cog-genomics.org/plink/2.0/ -(C) 2005-2023 Shaun Purcell, Christopher Chang GNU General Public License v3 -Logging to /scratch/prj/oliverpainfel/tmp/RtmpkiaRAY/file4f865f43e5af.log. +PLINK v2.00a5.12LM 64-bit Intel (25 Jun 2024) www.cog-genomics.org/plink/2.0/ +(C) 2005-2024 Shaun Purcell, Christopher Chang GNU General Public License v3 +Logging to /scratch/prj/oliverpainfel/tmp/Rtmp72Ly9F/fileda0422829e6a.log. Options in effect: --geno 0.02 --memory 4000 - --out /scratch/prj/oliverpainfel/tmp/RtmpkiaRAY/file4f865f43e5af + --out /scratch/prj/oliverpainfel/tmp/Rtmp72Ly9F/fileda0422829e6a --pfile misc/dev/test_data/output/example_plink2/geno/example_plink2.ref.chr22 --threads 1 --write-snplist -Start time: Thu Jul 25 09:40:31 2024 -1031702 MiB RAM detected, ~1018678 available; reserving 4000 MiB for main +Start time: Thu Jul 25 15:07:07 2024 +1031702 MiB RAM detected, ~1018340 available; reserving 4000 MiB for main workspace. Using 1 compute thread. 12 samples (5 females, 7 males; 12 founders) loaded from @@ -88,23 +95,23 @@ Calculating allele frequencies... 0%done. --geno: 10 variants removed due to missing genotype data. 990 variants remaining after main filters. --write-snplist: Variant IDs written to -/scratch/prj/oliverpainfel/tmp/RtmpkiaRAY/file4f865f43e5af.snplist . -End time: Thu Jul 25 09:40:31 2024 -PLINK v2.00a5LM 64-bit Intel (23 Sep 2023) www.cog-genomics.org/plink/2.0/ -(C) 2005-2023 Shaun Purcell, Christopher Chang GNU General Public License v3 -Logging to /scratch/prj/oliverpainfel/tmp/RtmpkiaRAY/file4f86fc0f143.log. +/scratch/prj/oliverpainfel/tmp/Rtmp72Ly9F/fileda0422829e6a.snplist . +End time: Thu Jul 25 15:07:07 2024 +PLINK v2.00a5.12LM 64-bit Intel (25 Jun 2024) www.cog-genomics.org/plink/2.0/ +(C) 2005-2024 Shaun Purcell, Christopher Chang GNU General Public License v3 +Logging to /scratch/prj/oliverpainfel/tmp/Rtmp72Ly9F/fileda047b48b11a.log. Options in effect: --geno 0.02 --hwe 1e-06 --maf 0.05 --memory 4000 - --out /scratch/prj/oliverpainfel/tmp/RtmpkiaRAY/file4f86fc0f143 + --out /scratch/prj/oliverpainfel/tmp/Rtmp72Ly9F/fileda047b48b11a --pfile misc/dev/test_data/ref/ref.chr22 --threads 1 --write-snplist -Start time: Thu Jul 25 09:40:31 2024 -1031702 MiB RAM detected, ~1018678 available; reserving 4000 MiB for main +Start time: Thu Jul 25 15:07:07 2024 +1031702 MiB RAM detected, ~1018339 available; reserving 4000 MiB for main workspace. Using 1 compute thread. 3313 samples (1568 females, 1745 males; 3313 founders) loaded from @@ -118,21 +125,21 @@ Calculating allele frequencies... 0%done. (--maf/--max-maf/--mac/--max-mac). 590 variants remaining after main filters. --write-snplist: Variant IDs written to -/scratch/prj/oliverpainfel/tmp/RtmpkiaRAY/file4f86fc0f143.snplist . -End time: Thu Jul 25 09:40:31 2024 -PLINK v2.00a5LM 64-bit Intel (23 Sep 2023) www.cog-genomics.org/plink/2.0/ -(C) 2005-2023 Shaun Purcell, Christopher Chang GNU General Public License v3 -Logging to /scratch/prj/oliverpainfel/tmp/RtmpkiaRAY/file4f866e7c64ba.chr22.log. +/scratch/prj/oliverpainfel/tmp/Rtmp72Ly9F/fileda047b48b11a.snplist . +End time: Thu Jul 25 15:07:07 2024 +PLINK v2.00a5.12LM 64-bit Intel (25 Jun 2024) www.cog-genomics.org/plink/2.0/ +(C) 2005-2024 Shaun Purcell, Christopher Chang GNU General Public License v3 +Logging to /scratch/prj/oliverpainfel/tmp/Rtmp72Ly9F/fileda04776c4b90.chr22.log. Options in effect: - --extract /scratch/prj/oliverpainfel/tmp/RtmpkiaRAY/file4f862466af51 + --extract /scratch/prj/oliverpainfel/tmp/Rtmp72Ly9F/fileda0435947818 --indep-pairwise 1000 5 0.2 --memory 4000 - --out /scratch/prj/oliverpainfel/tmp/RtmpkiaRAY/file4f866e7c64ba.chr22 + --out /scratch/prj/oliverpainfel/tmp/Rtmp72Ly9F/fileda04776c4b90.chr22 --pfile misc/dev/test_data/ref/ref.chr22 --threads 1 -Start time: Thu Jul 25 09:40:31 2024 -1031702 MiB RAM detected, ~1018672 available; reserving 4000 MiB for main +Start time: Thu Jul 25 15:07:07 2024 +1031702 MiB RAM detected, ~1018334 available; reserving 4000 MiB for main workspace. Using 1 compute thread. 3313 samples (1568 females, 1745 males; 3313 founders) loaded from @@ -144,22 +151,22 @@ Calculating allele frequencies... 0%done. 587 variants remaining after main filters. --indep-pairwise (1 compute thread): 0%50%415/587 variants removed. Writing... Variant lists written to -/scratch/prj/oliverpainfel/tmp/RtmpkiaRAY/file4f866e7c64ba.chr22.prune.in and -/scratch/prj/oliverpainfel/tmp/RtmpkiaRAY/file4f866e7c64ba.chr22.prune.out . -End time: Thu Jul 25 09:40:31 2024 -PLINK v2.00a5LM 64-bit Intel (23 Sep 2023) www.cog-genomics.org/plink/2.0/ -(C) 2005-2023 Shaun Purcell, Christopher Chang GNU General Public License v3 -Logging to /scratch/prj/oliverpainfel/tmp/RtmpkiaRAY/ref_subset_chr22.log. +/scratch/prj/oliverpainfel/tmp/Rtmp72Ly9F/fileda04776c4b90.chr22.prune.in and +/scratch/prj/oliverpainfel/tmp/Rtmp72Ly9F/fileda04776c4b90.chr22.prune.out . +End time: Thu Jul 25 15:07:08 2024 +PLINK v2.00a5.12LM 64-bit Intel (25 Jun 2024) www.cog-genomics.org/plink/2.0/ +(C) 2005-2024 Shaun Purcell, Christopher Chang GNU General Public License v3 +Logging to /scratch/prj/oliverpainfel/tmp/Rtmp72Ly9F/ref_subset_chr22.log. Options in effect: - --extract /scratch/prj/oliverpainfel/tmp/RtmpkiaRAY/file4f8610370ef + --extract /scratch/prj/oliverpainfel/tmp/Rtmp72Ly9F/fileda043c8175bb --make-pgen --memory 4000 - --out /scratch/prj/oliverpainfel/tmp/RtmpkiaRAY/ref_subset_chr22 + --out /scratch/prj/oliverpainfel/tmp/Rtmp72Ly9F/ref_subset_chr22 --pfile misc/dev/test_data/ref/ref.chr22 --threads 1 -Start time: Thu Jul 25 09:40:31 2024 -1031702 MiB RAM detected, ~1018665 available; reserving 4000 MiB for main +Start time: Thu Jul 25 15:07:08 2024 +1031702 MiB RAM detected, ~1018330 available; reserving 4000 MiB for main workspace. Using 1 compute thread. 3313 samples (1568 females, 1745 males; 3313 founders) loaded from @@ -168,81 +175,81 @@ misc/dev/test_data/ref/ref.chr22.psam. 3 categorical phenotypes loaded. --extract: 172 variants remaining. 172 variants remaining after main filters. -Writing /scratch/prj/oliverpainfel/tmp/RtmpkiaRAY/ref_subset_chr22.psam ... +Writing /scratch/prj/oliverpainfel/tmp/Rtmp72Ly9F/ref_subset_chr22.psam ... done. -Writing /scratch/prj/oliverpainfel/tmp/RtmpkiaRAY/ref_subset_chr22.pvar ... +Writing /scratch/prj/oliverpainfel/tmp/Rtmp72Ly9F/ref_subset_chr22.pvar ... 0%0%1%1%2%2%3%4%4%5%5%6%6%7%8%8%9%9%10%11%11%12%12%13%13%14%15%15%16%16%17%18%18%19%19%20%20%21%22%22%23%23%24%25%25%26%26%27%27%28%29%29%30%30%31%31%32%33%33%34%34%35%36%36%37%37%38%38%39%40%40%41%41%42%43%43%44%44%45%45%46%47%47%48%48%49%50%50%51%51%52%52%53%54%54%55%55%56%56%57%58%58%59%59%60%61%61%62%62%63%63%64%65%65%66%66%67%68%68%69%69%70%70%71%72%72%73%73%74%75%75%76%76%77%77%78%79%79%80%80%81%81%82%83%83%84%84%85%86%86%87%87%88%88%89%90%90%91%91%92%93%93%94%94%95%95%96%97%97%98%98%99%done. -Writing /scratch/prj/oliverpainfel/tmp/RtmpkiaRAY/ref_subset_chr22.pgen ... +Writing /scratch/prj/oliverpainfel/tmp/Rtmp72Ly9F/ref_subset_chr22.pgen ... 0%done. -End time: Thu Jul 25 09:40:31 2024 -PLINK v2.00a5LM 64-bit Intel (23 Sep 2023) www.cog-genomics.org/plink/2.0/ -(C) 2005-2023 Shaun Purcell, Christopher Chang GNU General Public License v3 -Logging to /scratch/prj/oliverpainfel/tmp/RtmpkiaRAY/ref_merge.log. +End time: Thu Jul 25 15:07:08 2024 +PLINK v2.00a5.12LM 64-bit Intel (25 Jun 2024) www.cog-genomics.org/plink/2.0/ +(C) 2005-2024 Shaun Purcell, Christopher Chang GNU General Public License v3 +Logging to /scratch/prj/oliverpainfel/tmp/Rtmp72Ly9F/ref_merge.log. Options in effect: - --extract /scratch/prj/oliverpainfel/tmp/RtmpkiaRAY/extract.snplist + --extract /scratch/prj/oliverpainfel/tmp/Rtmp72Ly9F/extract.snplist --make-pgen --memory 4000 - --out /scratch/prj/oliverpainfel/tmp/RtmpkiaRAY/ref_merge - --pfile /scratch/prj/oliverpainfel/tmp/RtmpkiaRAY/ref_subset_chr22 + --out /scratch/prj/oliverpainfel/tmp/Rtmp72Ly9F/ref_merge + --pfile /scratch/prj/oliverpainfel/tmp/Rtmp72Ly9F/ref_subset_chr22 --threads 1 -Start time: Thu Jul 25 09:40:31 2024 -1031702 MiB RAM detected, ~1018665 available; reserving 4000 MiB for main +Start time: Thu Jul 25 15:07:08 2024 +1031702 MiB RAM detected, ~1018330 available; reserving 4000 MiB for main workspace. Using 1 compute thread. 3313 samples (1568 females, 1745 males; 3313 founders) loaded from -/scratch/prj/oliverpainfel/tmp/RtmpkiaRAY/ref_subset_chr22.psam. +/scratch/prj/oliverpainfel/tmp/Rtmp72Ly9F/ref_subset_chr22.psam. 172 variants loaded from -/scratch/prj/oliverpainfel/tmp/RtmpkiaRAY/ref_subset_chr22.pvar. +/scratch/prj/oliverpainfel/tmp/Rtmp72Ly9F/ref_subset_chr22.pvar. 3 categorical phenotypes loaded. --extract: 172 variants remaining. 172 variants remaining after main filters. -Writing /scratch/prj/oliverpainfel/tmp/RtmpkiaRAY/ref_merge.psam ... done. -Writing /scratch/prj/oliverpainfel/tmp/RtmpkiaRAY/ref_merge.pvar ... 0%0%1%1%2%2%3%4%4%5%5%6%6%7%8%8%9%9%10%11%11%12%12%13%13%14%15%15%16%16%17%18%18%19%19%20%20%21%22%22%23%23%24%25%25%26%26%27%27%28%29%29%30%30%31%31%32%33%33%34%34%35%36%36%37%37%38%38%39%40%40%41%41%42%43%43%44%44%45%45%46%47%47%48%48%49%50%50%51%51%52%52%53%54%54%55%55%56%56%57%58%58%59%59%60%61%61%62%62%63%63%64%65%65%66%66%67%68%68%69%69%70%70%71%72%72%73%73%74%75%75%76%76%77%77%78%79%79%80%80%81%81%82%83%83%84%84%85%86%86%87%87%88%88%89%90%90%91%91%92%93%93%94%94%95%95%96%97%97%98%98%99%done. -Writing /scratch/prj/oliverpainfel/tmp/RtmpkiaRAY/ref_merge.pgen ... 0%done. -End time: Thu Jul 25 09:40:31 2024 -PLINK v2.00a5LM 64-bit Intel (23 Sep 2023) www.cog-genomics.org/plink/2.0/ -(C) 2005-2023 Shaun Purcell, Christopher Chang GNU General Public License v3 -Logging to /scratch/prj/oliverpainfel/tmp/RtmpkiaRAY/ref_merge.log. +Writing /scratch/prj/oliverpainfel/tmp/Rtmp72Ly9F/ref_merge.psam ... done. +Writing /scratch/prj/oliverpainfel/tmp/Rtmp72Ly9F/ref_merge.pvar ... 0%0%1%1%2%2%3%4%4%5%5%6%6%7%8%8%9%9%10%11%11%12%12%13%13%14%15%15%16%16%17%18%18%19%19%20%20%21%22%22%23%23%24%25%25%26%26%27%27%28%29%29%30%30%31%31%32%33%33%34%34%35%36%36%37%37%38%38%39%40%40%41%41%42%43%43%44%44%45%45%46%47%47%48%48%49%50%50%51%51%52%52%53%54%54%55%55%56%56%57%58%58%59%59%60%61%61%62%62%63%63%64%65%65%66%66%67%68%68%69%69%70%70%71%72%72%73%73%74%75%75%76%76%77%77%78%79%79%80%80%81%81%82%83%83%84%84%85%86%86%87%87%88%88%89%90%90%91%91%92%93%93%94%94%95%95%96%97%97%98%98%99%done. +Writing /scratch/prj/oliverpainfel/tmp/Rtmp72Ly9F/ref_merge.pgen ... 0%done. +End time: Thu Jul 25 15:07:08 2024 +PLINK v2.00a5.12LM 64-bit Intel (25 Jun 2024) www.cog-genomics.org/plink/2.0/ +(C) 2005-2024 Shaun Purcell, Christopher Chang GNU General Public License v3 +Logging to /scratch/prj/oliverpainfel/tmp/Rtmp72Ly9F/ref_merge.log. Options in effect: --memory 4000 - --out /scratch/prj/oliverpainfel/tmp/RtmpkiaRAY/ref_merge + --out /scratch/prj/oliverpainfel/tmp/Rtmp72Ly9F/ref_merge --pca 6 biallelic-var-wts - --pfile /scratch/prj/oliverpainfel/tmp/RtmpkiaRAY/ref_merge + --pfile /scratch/prj/oliverpainfel/tmp/Rtmp72Ly9F/ref_merge --threads 1 -Start time: Thu Jul 25 09:40:32 2024 -1031702 MiB RAM detected, ~1018665 available; reserving 4000 MiB for main +Start time: Thu Jul 25 15:07:08 2024 +1031702 MiB RAM detected, ~1018330 available; reserving 4000 MiB for main workspace. Using 1 compute thread. 3313 samples (1568 females, 1745 males; 3313 founders) loaded from -/scratch/prj/oliverpainfel/tmp/RtmpkiaRAY/ref_merge.psam. +/scratch/prj/oliverpainfel/tmp/Rtmp72Ly9F/ref_merge.psam. 172 variants loaded from -/scratch/prj/oliverpainfel/tmp/RtmpkiaRAY/ref_merge.pvar. +/scratch/prj/oliverpainfel/tmp/Rtmp72Ly9F/ref_merge.pvar. 3 categorical phenotypes loaded. Calculating allele frequencies... 0%done. Constructing GRM: 0%83%done. Correcting for missingness... 0%done. Extracting eigenvalues and eigenvectors... done. --pca: Variant weights written to -/scratch/prj/oliverpainfel/tmp/RtmpkiaRAY/ref_merge.eigenvec.var . +/scratch/prj/oliverpainfel/tmp/Rtmp72Ly9F/ref_merge.eigenvec.var . --pca: Eigenvectors written to -/scratch/prj/oliverpainfel/tmp/RtmpkiaRAY/ref_merge.eigenvec , and eigenvalues -written to /scratch/prj/oliverpainfel/tmp/RtmpkiaRAY/ref_merge.eigenval . -End time: Thu Jul 25 09:40:38 2024 -PLINK v2.00a5LM 64-bit Intel (23 Sep 2023) www.cog-genomics.org/plink/2.0/ -(C) 2005-2023 Shaun Purcell, Christopher Chang GNU General Public License v3 -Logging to /scratch/prj/oliverpainfel/tmp/RtmpkiaRAY/profiles.chr22.log. +/scratch/prj/oliverpainfel/tmp/Rtmp72Ly9F/ref_merge.eigenvec , and eigenvalues +written to /scratch/prj/oliverpainfel/tmp/Rtmp72Ly9F/ref_merge.eigenval . +End time: Thu Jul 25 15:07:13 2024 +PLINK v2.00a5.12LM 64-bit Intel (25 Jun 2024) www.cog-genomics.org/plink/2.0/ +(C) 2005-2024 Shaun Purcell, Christopher Chang GNU General Public License v3 +Logging to /scratch/prj/oliverpainfel/tmp/Rtmp72Ly9F/profiles.chr22.log. Options in effect: --chr 22 - --out /scratch/prj/oliverpainfel/tmp/RtmpkiaRAY/profiles.chr22 + --out /scratch/prj/oliverpainfel/tmp/Rtmp72Ly9F/profiles.chr22 --pfile misc/dev/test_data/ref/ref.chr22 - --score /scratch/prj/oliverpainfel/tmp/RtmpkiaRAY/ref.eigenvec.var header-read no-mean-imputation cols=+scoresums,-scoreavgs + --score /scratch/prj/oliverpainfel/tmp/Rtmp72Ly9F/ref.eigenvec.var header-read no-mean-imputation cols=+scoresums,-scoreavgs --score-col-nums 4-9 --threads 1 -Start time: Thu Jul 25 09:40:38 2024 -1031702 MiB RAM detected, ~1018673 available; reserving 515851 MiB for main +Start time: Thu Jul 25 15:07:13 2024 +1031702 MiB RAM detected, ~1018335 available; reserving 515851 MiB for main workspace. Using 1 compute thread. 3313 samples (1568 females, 1745 males; 3313 founders) loaded from @@ -251,24 +258,24 @@ misc/dev/test_data/ref/ref.chr22.psam. 3 categorical phenotypes loaded. --score: 172 variants processed. --score: Results written to -/scratch/prj/oliverpainfel/tmp/RtmpkiaRAY/profiles.chr22.sscore . -End time: Thu Jul 25 09:40:38 2024 +/scratch/prj/oliverpainfel/tmp/Rtmp72Ly9F/profiles.chr22.sscore . +End time: Thu Jul 25 15:07:13 2024 Warning message: In nominalTrainWorkflow(x = x, y = y, wts = weights, info = trainInfo, : There were missing values in resampled performance measures. -PLINK v2.00a5LM 64-bit Intel (23 Sep 2023) www.cog-genomics.org/plink/2.0/ -(C) 2005-2023 Shaun Purcell, Christopher Chang GNU General Public License v3 -Logging to /scratch/prj/oliverpainfel/tmp/RtmpkiaRAY/profiles.chr22.log. +PLINK v2.00a5.12LM 64-bit Intel (25 Jun 2024) www.cog-genomics.org/plink/2.0/ +(C) 2005-2024 Shaun Purcell, Christopher Chang GNU General Public License v3 +Logging to /scratch/prj/oliverpainfel/tmp/Rtmp72Ly9F/profiles.chr22.log. Options in effect: --chr 22 - --out /scratch/prj/oliverpainfel/tmp/RtmpkiaRAY/profiles.chr22 + --out /scratch/prj/oliverpainfel/tmp/Rtmp72Ly9F/profiles.chr22 --pfile misc/dev/test_data/output/example_plink2/geno/example_plink2.ref.chr22 - --score /scratch/prj/oliverpainfel/tmp/RtmpkiaRAY/ref.eigenvec.var header-read no-mean-imputation cols=+scoresums,-scoreavgs + --score /scratch/prj/oliverpainfel/tmp/Rtmp72Ly9F/ref.eigenvec.var header-read no-mean-imputation cols=+scoresums,-scoreavgs --score-col-nums 4-9 --threads 1 -Start time: Thu Jul 25 09:40:43 2024 -1031702 MiB RAM detected, ~1018644 available; reserving 515851 MiB for main +Start time: Thu Jul 25 15:07:18 2024 +1031702 MiB RAM detected, ~1018312 available; reserving 515851 MiB for main workspace. Using 1 compute thread. 12 samples (5 females, 7 males; 12 founders) loaded from @@ -278,7 +285,7 @@ misc/dev/test_data/output/example_plink2/geno/example_plink2.ref.chr22.pvar. Note: No phenotype data present. --score: 172 variants processed. --score: Results written to -/scratch/prj/oliverpainfel/tmp/RtmpkiaRAY/profiles.chr22.sscore . -End time: Thu Jul 25 09:40:43 2024 +/scratch/prj/oliverpainfel/tmp/Rtmp72Ly9F/profiles.chr22.sscore . +End time: Thu Jul 25 15:07:18 2024 null device 1 diff --git a/pipeline/misc/dev/test_data/output/reference/logs/ancestry_reporter-example_plink2.log b/pipeline/misc/dev/test_data/output/reference/logs/ancestry_reporter-example_plink2.log index e69de29..46b320d 100644 --- a/pipeline/misc/dev/test_data/output/reference/logs/ancestry_reporter-example_plink2.log +++ b/pipeline/misc/dev/test_data/output/reference/logs/ancestry_reporter-example_plink2.log @@ -0,0 +1,7 @@ +During startup - Warning messages: +1: Setting LC_COLLATE failed, using "C" +2: Setting LC_TIME failed, using "C" +3: Setting LC_MESSAGES failed, using "C" +4: Setting LC_MONETARY failed, using "C" +5: Setting LC_PAPER failed, using "C" +6: Setting LC_MEASUREMENT failed, using "C" diff --git a/pipeline/misc/dev/test_data/output/reference/logs/format_target_i-example_plink2-22.log b/pipeline/misc/dev/test_data/output/reference/logs/format_target_i-example_plink2-22.log index 89bd48b..0c7fd42 100644 --- a/pipeline/misc/dev/test_data/output/reference/logs/format_target_i-example_plink2-22.log +++ b/pipeline/misc/dev/test_data/output/reference/logs/format_target_i-example_plink2-22.log @@ -1,16 +1,23 @@ -PLINK v2.00a5LM 64-bit Intel (23 Sep 2023) www.cog-genomics.org/plink/2.0/ -(C) 2005-2023 Shaun Purcell, Christopher Chang GNU General Public License v3 -Logging to /scratch/prj/oliverpainfel/tmp/RtmpClbFKL/subset.log. +During startup - Warning messages: +1: Setting LC_COLLATE failed, using "C" +2: Setting LC_TIME failed, using "C" +3: Setting LC_MESSAGES failed, using "C" +4: Setting LC_MONETARY failed, using "C" +5: Setting LC_PAPER failed, using "C" +6: Setting LC_MEASUREMENT failed, using "C" +PLINK v2.00a5.12LM 64-bit Intel (25 Jun 2024) www.cog-genomics.org/plink/2.0/ +(C) 2005-2024 Shaun Purcell, Christopher Chang GNU General Public License v3 +Logging to /scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/subset.log. Options in effect: - --extract /scratch/prj/oliverpainfel/tmp/RtmpClbFKL/extract_list_1.txt + --extract /scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/extract_list_1.txt --make-pgen pvar-cols= --memory 5000 - --out /scratch/prj/oliverpainfel/tmp/RtmpClbFKL/subset + --out /scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/subset --pfile misc/dev/test_data/target/example.chr22 --threads 1 -Start time: Thu Jul 25 09:40:21 2024 -1031702 MiB RAM detected, ~1018887 available; reserving 5000 MiB for main +Start time: Thu Jul 25 15:07:01 2024 +1031702 MiB RAM detected, ~1018563 available; reserving 5000 MiB for main workspace. Using 1 compute thread. 12 samples (5 females, 7 males; 12 founders) loaded from @@ -19,51 +26,51 @@ misc/dev/test_data/target/example.chr22.psam. Note: No phenotype data present. --extract: 1000 variants remaining. 1000 variants remaining after main filters. -Writing /scratch/prj/oliverpainfel/tmp/RtmpClbFKL/subset.psam ... done. -Writing /scratch/prj/oliverpainfel/tmp/RtmpClbFKL/subset.pvar ... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done. -Writing /scratch/prj/oliverpainfel/tmp/RtmpClbFKL/subset.pgen ... 0%done. -End time: Thu Jul 25 09:40:21 2024 -PLINK v2.00a5LM 64-bit Intel (23 Sep 2023) www.cog-genomics.org/plink/2.0/ -(C) 2005-2023 Shaun Purcell, Christopher Chang GNU General Public License v3 -Logging to /scratch/prj/oliverpainfel/tmp/RtmpClbFKL/subset.log. +Writing /scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/subset.psam ... done. +Writing /scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/subset.pvar ... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done. +Writing /scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/subset.pgen ... 0%done. +End time: Thu Jul 25 15:07:01 2024 +PLINK v2.00a5.12LM 64-bit Intel (25 Jun 2024) www.cog-genomics.org/plink/2.0/ +(C) 2005-2024 Shaun Purcell, Christopher Chang GNU General Public License v3 +Logging to /scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/subset.log. Options in effect: - --extract /scratch/prj/oliverpainfel/tmp/RtmpClbFKL/extract_list_2.txt + --extract /scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/extract_list_2.txt --make-pgen --memory 5000 - --out /scratch/prj/oliverpainfel/tmp/RtmpClbFKL/subset - --pfile /scratch/prj/oliverpainfel/tmp/RtmpClbFKL/subset + --out /scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/subset + --pfile /scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/subset --threads 1 -Start time: Thu Jul 25 09:40:21 2024 -1031702 MiB RAM detected, ~1018885 available; reserving 5000 MiB for main +Start time: Thu Jul 25 15:07:01 2024 +1031702 MiB RAM detected, ~1018561 available; reserving 5000 MiB for main workspace. Using 1 compute thread. Warning: --make-pgen input and output filenames match. Appending '~' to input filenames. 12 samples (5 females, 7 males; 12 founders) loaded from -/scratch/prj/oliverpainfel/tmp/RtmpClbFKL/subset.psam~. +/scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/subset.psam~. 1000 variants loaded from -/scratch/prj/oliverpainfel/tmp/RtmpClbFKL/subset.pvar~. +/scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/subset.pvar~. Note: No phenotype data present. --extract: 1000 variants remaining. 1000 variants remaining after main filters. -Writing /scratch/prj/oliverpainfel/tmp/RtmpClbFKL/subset.psam ... done. -Writing /scratch/prj/oliverpainfel/tmp/RtmpClbFKL/subset.pvar ... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done. -Writing /scratch/prj/oliverpainfel/tmp/RtmpClbFKL/subset.pgen ... 0%done. -End time: Thu Jul 25 09:40:21 2024 -PLINK v2.00a5LM 64-bit Intel (23 Sep 2023) www.cog-genomics.org/plink/2.0/ -(C) 2005-2023 Shaun Purcell, Christopher Chang GNU General Public License v3 -Logging to /scratch/prj/oliverpainfel/tmp/RtmpClbFKL/REF.log. +Writing /scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/subset.psam ... done. +Writing /scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/subset.pvar ... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done. +Writing /scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/subset.pgen ... 0%done. +End time: Thu Jul 25 15:07:01 2024 +PLINK v2.00a5.12LM 64-bit Intel (25 Jun 2024) www.cog-genomics.org/plink/2.0/ +(C) 2005-2024 Shaun Purcell, Christopher Chang GNU General Public License v3 +Logging to /scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/REF.log. Options in effect: --make-pgen --memory 5000 - --out /scratch/prj/oliverpainfel/tmp/RtmpClbFKL/REF + --out /scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/REF --pfile misc/dev/test_data/ref/ref.chr22 --threads 1 - --update-ids /scratch/prj/oliverpainfel/tmp/RtmpClbFKL/ref_ID_update.txt + --update-ids /scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/ref_ID_update.txt -Start time: Thu Jul 25 09:40:21 2024 -1031702 MiB RAM detected, ~1018884 available; reserving 5000 MiB for main +Start time: Thu Jul 25 15:07:01 2024 +1031702 MiB RAM detected, ~1018560 available; reserving 5000 MiB for main workspace. Using 1 compute thread. 3313 samples (1568 females, 1745 males; 3313 founders) loaded from @@ -71,79 +78,79 @@ misc/dev/test_data/ref/ref.chr22.psam. 1000 variants loaded from misc/dev/test_data/ref/ref.chr22.pvar. 3 categorical phenotypes loaded. --update-ids: 3313 samples updated. -Writing /scratch/prj/oliverpainfel/tmp/RtmpClbFKL/REF.psam ... done. -Writing /scratch/prj/oliverpainfel/tmp/RtmpClbFKL/REF.pvar ... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done. -Writing /scratch/prj/oliverpainfel/tmp/RtmpClbFKL/REF.pgen ... 0%done. -End time: Thu Jul 25 09:40:21 2024 -PLINK v2.00a5LM 64-bit Intel (23 Sep 2023) www.cog-genomics.org/plink/2.0/ -(C) 2005-2023 Shaun Purcell, Christopher Chang GNU General Public License v3 -Logging to /scratch/prj/oliverpainfel/tmp/RtmpClbFKL/subset.log. +Writing /scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/REF.psam ... done. +Writing /scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/REF.pvar ... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done. +Writing /scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/REF.pgen ... 0%done. +End time: Thu Jul 25 15:07:01 2024 +PLINK v2.00a5.12LM 64-bit Intel (25 Jun 2024) www.cog-genomics.org/plink/2.0/ +(C) 2005-2024 Shaun Purcell, Christopher Chang GNU General Public License v3 +Logging to /scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/subset.log. Options in effect: --make-bed --memory 5000 - --out /scratch/prj/oliverpainfel/tmp/RtmpClbFKL/subset - --pfile /scratch/prj/oliverpainfel/tmp/RtmpClbFKL/subset + --out /scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/subset + --pfile /scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/subset --threads 1 -Start time: Thu Jul 25 09:40:22 2024 -1031702 MiB RAM detected, ~1018875 available; reserving 5000 MiB for main +Start time: Thu Jul 25 15:07:01 2024 +1031702 MiB RAM detected, ~1018552 available; reserving 5000 MiB for main workspace. Using 1 compute thread. 12 samples (5 females, 7 males; 12 founders) loaded from -/scratch/prj/oliverpainfel/tmp/RtmpClbFKL/subset.psam. +/scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/subset.psam. 1000 variants loaded from -/scratch/prj/oliverpainfel/tmp/RtmpClbFKL/subset.pvar. +/scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/subset.pvar. Note: No phenotype data present. -Writing /scratch/prj/oliverpainfel/tmp/RtmpClbFKL/subset.fam ... done. -Writing /scratch/prj/oliverpainfel/tmp/RtmpClbFKL/subset.bim ... done. -Writing /scratch/prj/oliverpainfel/tmp/RtmpClbFKL/subset.bed ... 0%done. -End time: Thu Jul 25 09:40:22 2024 -PLINK v2.00a5LM 64-bit Intel (23 Sep 2023) www.cog-genomics.org/plink/2.0/ -(C) 2005-2023 Shaun Purcell, Christopher Chang GNU General Public License v3 -Logging to /scratch/prj/oliverpainfel/tmp/RtmpClbFKL/REF.log. +Writing /scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/subset.fam ... done. +Writing /scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/subset.bim ... done. +Writing /scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/subset.bed ... 0%done. +End time: Thu Jul 25 15:07:01 2024 +PLINK v2.00a5.12LM 64-bit Intel (25 Jun 2024) www.cog-genomics.org/plink/2.0/ +(C) 2005-2024 Shaun Purcell, Christopher Chang GNU General Public License v3 +Logging to /scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/REF.log. Options in effect: --make-bed --memory 5000 - --out /scratch/prj/oliverpainfel/tmp/RtmpClbFKL/REF - --pfile /scratch/prj/oliverpainfel/tmp/RtmpClbFKL/REF + --out /scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/REF + --pfile /scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/REF --threads 1 -Start time: Thu Jul 25 09:40:22 2024 -1031702 MiB RAM detected, ~1018875 available; reserving 5000 MiB for main +Start time: Thu Jul 25 15:07:01 2024 +1031702 MiB RAM detected, ~1018552 available; reserving 5000 MiB for main workspace. Using 1 compute thread. 3313 samples (1568 females, 1745 males; 3313 founders) loaded from -/scratch/prj/oliverpainfel/tmp/RtmpClbFKL/REF.psam. -1000 variants loaded from /scratch/prj/oliverpainfel/tmp/RtmpClbFKL/REF.pvar. +/scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/REF.psam. +1000 variants loaded from /scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/REF.pvar. 3 categorical phenotypes loaded. -Writing /scratch/prj/oliverpainfel/tmp/RtmpClbFKL/REF.fam ... done. -Writing /scratch/prj/oliverpainfel/tmp/RtmpClbFKL/REF.bim ... done. -Writing /scratch/prj/oliverpainfel/tmp/RtmpClbFKL/REF.bed ... 0%done. -End time: Thu Jul 25 09:40:22 2024 +Writing /scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/REF.fam ... done. +Writing /scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/REF.bim ... done. +Writing /scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/REF.bed ... 0%done. +End time: Thu Jul 25 15:07:01 2024 PLINK v1.90b6.21 64-bit (19 Oct 2020) www.cog-genomics.org/plink/1.9/ (C) 2005-2020 Shaun Purcell, Christopher Chang GNU General Public License v3 -Logging to /scratch/prj/oliverpainfel/tmp/RtmpClbFKL/ref_targ.log. +Logging to /scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/ref_targ.log. Options in effect: --allow-no-sex - --bfile /scratch/prj/oliverpainfel/tmp/RtmpClbFKL/subset - --bmerge /scratch/prj/oliverpainfel/tmp/RtmpClbFKL/REF + --bfile /scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/subset + --bmerge /scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/REF --make-bed - --out /scratch/prj/oliverpainfel/tmp/RtmpClbFKL/ref_targ + --out /scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/ref_targ 1031702 MB RAM detected; reserving 515851 MB for main workspace. -12 people loaded from /scratch/prj/oliverpainfel/tmp/RtmpClbFKL/subset.fam. +12 people loaded from /scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/subset.fam. 3313 people to be merged from -/scratch/prj/oliverpainfel/tmp/RtmpClbFKL/REF.fam. +/scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/REF.fam. Of these, 3313 are new, while 0 are present in the base dataset. -1000 markers loaded from /scratch/prj/oliverpainfel/tmp/RtmpClbFKL/subset.bim. +1000 markers loaded from /scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/subset.bim. 1000 markers to be merged from -/scratch/prj/oliverpainfel/tmp/RtmpClbFKL/REF.bim. +/scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/REF.bim. Of these, 0 are new, while 1000 are present in the base dataset. Performing single-pass merge (3325 people, 1000 variants). Pass 1: fileset #1 complete. Merged fileset written to -/scratch/prj/oliverpainfel/tmp/RtmpClbFKL/ref_targ-merge.bed + -/scratch/prj/oliverpainfel/tmp/RtmpClbFKL/ref_targ-merge.bim + -/scratch/prj/oliverpainfel/tmp/RtmpClbFKL/ref_targ-merge.fam . +/scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/ref_targ-merge.bed + +/scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/ref_targ-merge.bim + +/scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/ref_targ-merge.fam . 1000 variants loaded from .bim file. 3325 people (1752 males, 1573 females) loaded from .fam. Using 1 thread (no multithreaded calculations invoked). @@ -152,28 +159,28 @@ Calculating allele frequencies... 0%1%2%3%4%5%6%7%8%9%10% Total genotyping rate is 0.998018. 1000 variants and 3325 people pass filters and QC. Note: No phenotypes present. ---make-bed to /scratch/prj/oliverpainfel/tmp/RtmpClbFKL/ref_targ.bed + -/scratch/prj/oliverpainfel/tmp/RtmpClbFKL/ref_targ.bim + -/scratch/prj/oliverpainfel/tmp/RtmpClbFKL/ref_targ.fam ... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done. -PLINK v2.00a5LM 64-bit Intel (23 Sep 2023) www.cog-genomics.org/plink/2.0/ -(C) 2005-2023 Shaun Purcell, Christopher Chang GNU General Public License v3 +--make-bed to /scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/ref_targ.bed + +/scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/ref_targ.bim + +/scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/ref_targ.fam ... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done. +PLINK v2.00a5.12LM 64-bit Intel (25 Jun 2024) www.cog-genomics.org/plink/2.0/ +(C) 2005-2024 Shaun Purcell, Christopher Chang GNU General Public License v3 Logging to misc/dev/test_data/output/example_plink2/geno/example_plink2.ref.chr22.log. Options in effect: - --bfile /scratch/prj/oliverpainfel/tmp/RtmpClbFKL/ref_targ + --bfile /scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/ref_targ --make-pgen --memory 5000 --out misc/dev/test_data/output/example_plink2/geno/example_plink2.ref.chr22 - --remove /scratch/prj/oliverpainfel/tmp/RtmpClbFKL/REF.psam + --remove /scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/REF.psam --threads 1 -Start time: Thu Jul 25 09:40:23 2024 -1031702 MiB RAM detected, ~1018874 available; reserving 5000 MiB for main +Start time: Thu Jul 25 15:07:01 2024 +1031702 MiB RAM detected, ~1018552 available; reserving 5000 MiB for main workspace. Using 1 compute thread. 3325 samples (1573 females, 1752 males; 3325 founders) loaded from -/scratch/prj/oliverpainfel/tmp/RtmpClbFKL/ref_targ.fam. +/scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/ref_targ.fam. 1000 variants loaded from -/scratch/prj/oliverpainfel/tmp/RtmpClbFKL/ref_targ.bim. +/scratch/prj/oliverpainfel/tmp/RtmpqFvaS6/ref_targ.bim. Note: No phenotype data present. --remove: 12 samples remaining. 12 samples (5 females, 7 males; 12 founders) remaining after main filters. @@ -186,4 +193,4 @@ misc/dev/test_data/output/example_plink2/geno/example_plink2.ref.chr22.pvar ... Writing misc/dev/test_data/output/example_plink2/geno/example_plink2.ref.chr22.pgen ... 0%done. -End time: Thu Jul 25 09:40:23 2024 +End time: Thu Jul 25 15:07:01 2024 diff --git a/pipeline/misc/dev/test_data/output/reference/logs/indiv_report_i-example_plink2-4_EAS.4_EAS.log b/pipeline/misc/dev/test_data/output/reference/logs/indiv_report_i-example_plink2-4_EAS.4_EAS.log index f18fbbe..00fb0b0 100644 --- a/pipeline/misc/dev/test_data/output/reference/logs/indiv_report_i-example_plink2-4_EAS.4_EAS.log +++ b/pipeline/misc/dev/test_data/output/reference/logs/indiv_report_i-example_plink2-4_EAS.4_EAS.log @@ -1,3 +1,10 @@ +During startup - Warning messages: +1: Setting LC_COLLATE failed, using "C" +2: Setting LC_TIME failed, using "C" +3: Setting LC_MESSAGES failed, using "C" +4: Setting LC_MONETARY failed, using "C" +5: Setting LC_PAPER failed, using "C" +6: Setting LC_MEASUREMENT failed, using "C" processing file: indiv_report_creator.Rmd @@ -38,6 +45,6 @@ processing file: indiv_report_creator.Rmd 35/35 output file: indiv_report_creator.knit.md -/scratch/prj/oliverpainfel/Software/MyGit/GenoPred/pipeline/.snakemake/conda/aea4ef260655c3bcc12fec8909f5f6dd_/bin/pandoc +RTS -K512m -RTS indiv_report_creator.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /scratch/prj/oliverpainfel/Software/MyGit/GenoPred/pipeline/misc/dev/test_data/output/example_plink2/reports/individual/example_plink2-4_EAS.4_EAS-report.html --lua-filter /scratch/prj/oliverpainfel/Software/MyGit/GenoPred/pipeline/.snakemake/conda/aea4ef260655c3bcc12fec8909f5f6dd_/lib/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /scratch/prj/oliverpainfel/Software/MyGit/GenoPred/pipeline/.snakemake/conda/aea4ef260655c3bcc12fec8909f5f6dd_/lib/R/library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /scratch/prj/oliverpainfel/Software/MyGit/GenoPred/pipeline/.snakemake/conda/aea4ef260655c3bcc12fec8909f5f6dd_/lib/R/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=cosmo --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /scratch/prj/oliverpainfel/tmp/RtmpcWpi3g/rmarkdown-stra4215b60410a.html +/tools/GenoPred/pipeline/.snakemake/conda/4e4fa1f1bb8db14f9a36511ee76ae12c_/bin/pandoc +RTS -K512m -RTS indiv_report_creator.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tools/GenoPred/pipeline/misc/dev/test_data/output/example_plink2/reports/individual/example_plink2-4_EAS.4_EAS-report.html --lua-filter /tools/GenoPred/pipeline/.snakemake/conda/4e4fa1f1bb8db14f9a36511ee76ae12c_/lib/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /tools/GenoPred/pipeline/.snakemake/conda/4e4fa1f1bb8db14f9a36511ee76ae12c_/lib/R/library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /tools/GenoPred/pipeline/.snakemake/conda/4e4fa1f1bb8db14f9a36511ee76ae12c_/lib/R/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=cosmo --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /scratch/prj/oliverpainfel/tmp/RtmpK1cCdC/rmarkdown-strde29529a506a.html Output created: misc/dev/test_data/output/example_plink2/reports/individual/example_plink2-4_EAS.4_EAS-report.html diff --git a/pipeline/misc/dev/test_data/output/reference/logs/pc_projection_i-example_plink2-AFR.log b/pipeline/misc/dev/test_data/output/reference/logs/pc_projection_i-example_plink2-AFR.log index 766d73a..c450882 100644 --- a/pipeline/misc/dev/test_data/output/reference/logs/pc_projection_i-example_plink2-AFR.log +++ b/pipeline/misc/dev/test_data/output/reference/logs/pc_projection_i-example_plink2-AFR.log @@ -1,18 +1,25 @@ -PLINK v2.00a5LM 64-bit Intel (23 Sep 2023) www.cog-genomics.org/plink/2.0/ -(C) 2005-2023 Shaun Purcell, Christopher Chang GNU General Public License v3 -Logging to /scratch/prj/oliverpainfel/tmp/RtmpYEldZb/profiles.chr22.log. +During startup - Warning messages: +1: Setting LC_COLLATE failed, using "C" +2: Setting LC_TIME failed, using "C" +3: Setting LC_MESSAGES failed, using "C" +4: Setting LC_MONETARY failed, using "C" +5: Setting LC_PAPER failed, using "C" +6: Setting LC_MEASUREMENT failed, using "C" +PLINK v2.00a5.12LM 64-bit Intel (25 Jun 2024) www.cog-genomics.org/plink/2.0/ +(C) 2005-2024 Shaun Purcell, Christopher Chang GNU General Public License v3 +Logging to /scratch/prj/oliverpainfel/tmp/RtmpIl9S1a/profiles.chr22.log. Options in effect: --chr 22 --keep misc/dev/test_data/output/example_plink2/ancestry/keep_files/model_based/AFR.keep - --out /scratch/prj/oliverpainfel/tmp/RtmpYEldZb/profiles.chr22 + --out /scratch/prj/oliverpainfel/tmp/RtmpIl9S1a/profiles.chr22 --pfile misc/dev/test_data/output/example_plink2/geno/example_plink2.ref.chr22 --read-freq misc/dev/test_data/ref/freq_files/AFR/ref.AFR.chr22.afreq --score misc/dev/test_data/output/resources/data/ref/pc_score_files/AFR/ref-AFR-pcs.eigenvec.var.gz header-read cols=+scoresums,-scoreavgs --score-col-nums 4-9 --threads 1 -Start time: Thu Jul 25 09:41:25 2024 -1031702 MiB RAM detected, ~1018918 available; reserving 515851 MiB for main +Start time: Thu Jul 25 15:07:20 2024 +1031702 MiB RAM detected, ~1018590 available; reserving 515851 MiB for main workspace. Using 1 compute thread. 12 samples (5 females, 7 males; 12 founders) loaded from @@ -26,5 +33,5 @@ Note: No phenotype data present. --read-freq: Frequencies for 1000 variants loaded. --score: 275 variants processed. --score: Results written to -/scratch/prj/oliverpainfel/tmp/RtmpYEldZb/profiles.chr22.sscore . -End time: Thu Jul 25 09:41:25 2024 +/scratch/prj/oliverpainfel/tmp/RtmpIl9S1a/profiles.chr22.sscore . +End time: Thu Jul 25 15:07:20 2024 diff --git a/pipeline/misc/dev/test_data/output/reference/logs/pc_projection_i-example_plink2-CSA.log b/pipeline/misc/dev/test_data/output/reference/logs/pc_projection_i-example_plink2-CSA.log index d50e53a..08e5b5d 100644 --- a/pipeline/misc/dev/test_data/output/reference/logs/pc_projection_i-example_plink2-CSA.log +++ b/pipeline/misc/dev/test_data/output/reference/logs/pc_projection_i-example_plink2-CSA.log @@ -1,18 +1,25 @@ -PLINK v2.00a5LM 64-bit Intel (23 Sep 2023) www.cog-genomics.org/plink/2.0/ -(C) 2005-2023 Shaun Purcell, Christopher Chang GNU General Public License v3 -Logging to /scratch/prj/oliverpainfel/tmp/Rtmp8Ql5Ym/profiles.chr22.log. +During startup - Warning messages: +1: Setting LC_COLLATE failed, using "C" +2: Setting LC_TIME failed, using "C" +3: Setting LC_MESSAGES failed, using "C" +4: Setting LC_MONETARY failed, using "C" +5: Setting LC_PAPER failed, using "C" +6: Setting LC_MEASUREMENT failed, using "C" +PLINK v2.00a5.12LM 64-bit Intel (25 Jun 2024) www.cog-genomics.org/plink/2.0/ +(C) 2005-2024 Shaun Purcell, Christopher Chang GNU General Public License v3 +Logging to /scratch/prj/oliverpainfel/tmp/RtmpKbRa6r/profiles.chr22.log. Options in effect: --chr 22 --keep misc/dev/test_data/output/example_plink2/ancestry/keep_files/model_based/CSA.keep - --out /scratch/prj/oliverpainfel/tmp/Rtmp8Ql5Ym/profiles.chr22 + --out /scratch/prj/oliverpainfel/tmp/RtmpKbRa6r/profiles.chr22 --pfile misc/dev/test_data/output/example_plink2/geno/example_plink2.ref.chr22 --read-freq misc/dev/test_data/ref/freq_files/CSA/ref.CSA.chr22.afreq --score misc/dev/test_data/output/resources/data/ref/pc_score_files/CSA/ref-CSA-pcs.eigenvec.var.gz header-read cols=+scoresums,-scoreavgs --score-col-nums 4-9 --threads 1 -Start time: Thu Jul 25 09:41:15 2024 -1031702 MiB RAM detected, ~1018921 available; reserving 515851 MiB for main +Start time: Thu Jul 25 15:07:22 2024 +1031702 MiB RAM detected, ~1018588 available; reserving 515851 MiB for main workspace. Using 1 compute thread. 12 samples (5 females, 7 males; 12 founders) loaded from @@ -26,5 +33,5 @@ Note: No phenotype data present. --read-freq: Frequencies for 1000 variants loaded. --score: 138 variants processed. --score: Results written to -/scratch/prj/oliverpainfel/tmp/Rtmp8Ql5Ym/profiles.chr22.sscore . -End time: Thu Jul 25 09:41:15 2024 +/scratch/prj/oliverpainfel/tmp/RtmpKbRa6r/profiles.chr22.sscore . +End time: Thu Jul 25 15:07:22 2024 diff --git a/pipeline/misc/dev/test_data/output/reference/logs/pc_projection_i-example_plink2-EAS.log b/pipeline/misc/dev/test_data/output/reference/logs/pc_projection_i-example_plink2-EAS.log index 7b2d062..3485a75 100644 --- a/pipeline/misc/dev/test_data/output/reference/logs/pc_projection_i-example_plink2-EAS.log +++ b/pipeline/misc/dev/test_data/output/reference/logs/pc_projection_i-example_plink2-EAS.log @@ -1,18 +1,25 @@ -PLINK v2.00a5LM 64-bit Intel (23 Sep 2023) www.cog-genomics.org/plink/2.0/ -(C) 2005-2023 Shaun Purcell, Christopher Chang GNU General Public License v3 -Logging to /scratch/prj/oliverpainfel/tmp/RtmpixbRKQ/profiles.chr22.log. +During startup - Warning messages: +1: Setting LC_COLLATE failed, using "C" +2: Setting LC_TIME failed, using "C" +3: Setting LC_MESSAGES failed, using "C" +4: Setting LC_MONETARY failed, using "C" +5: Setting LC_PAPER failed, using "C" +6: Setting LC_MEASUREMENT failed, using "C" +PLINK v2.00a5.12LM 64-bit Intel (25 Jun 2024) www.cog-genomics.org/plink/2.0/ +(C) 2005-2024 Shaun Purcell, Christopher Chang GNU General Public License v3 +Logging to /scratch/prj/oliverpainfel/tmp/RtmpQSRrHC/profiles.chr22.log. Options in effect: --chr 22 --keep misc/dev/test_data/output/example_plink2/ancestry/keep_files/model_based/EAS.keep - --out /scratch/prj/oliverpainfel/tmp/RtmpixbRKQ/profiles.chr22 + --out /scratch/prj/oliverpainfel/tmp/RtmpQSRrHC/profiles.chr22 --pfile misc/dev/test_data/output/example_plink2/geno/example_plink2.ref.chr22 --read-freq misc/dev/test_data/ref/freq_files/EAS/ref.EAS.chr22.afreq --score misc/dev/test_data/output/resources/data/ref/pc_score_files/EAS/ref-EAS-pcs.eigenvec.var.gz header-read cols=+scoresums,-scoreavgs --score-col-nums 4-9 --threads 1 -Start time: Thu Jul 25 09:41:08 2024 -1031702 MiB RAM detected, ~1018922 available; reserving 515851 MiB for main +Start time: Thu Jul 25 15:07:22 2024 +1031702 MiB RAM detected, ~1018589 available; reserving 515851 MiB for main workspace. Using 1 compute thread. 12 samples (5 females, 7 males; 12 founders) loaded from @@ -26,5 +33,5 @@ Note: No phenotype data present. --read-freq: Frequencies for 1000 variants loaded. --score: 133 variants processed. --score: Results written to -/scratch/prj/oliverpainfel/tmp/RtmpixbRKQ/profiles.chr22.sscore . -End time: Thu Jul 25 09:41:08 2024 +/scratch/prj/oliverpainfel/tmp/RtmpQSRrHC/profiles.chr22.sscore . +End time: Thu Jul 25 15:07:22 2024 diff --git a/pipeline/misc/dev/test_data/output/reference/logs/pc_projection_i-example_plink2-EUR.log b/pipeline/misc/dev/test_data/output/reference/logs/pc_projection_i-example_plink2-EUR.log index 541377c..dc730db 100644 --- a/pipeline/misc/dev/test_data/output/reference/logs/pc_projection_i-example_plink2-EUR.log +++ b/pipeline/misc/dev/test_data/output/reference/logs/pc_projection_i-example_plink2-EUR.log @@ -1,18 +1,25 @@ -PLINK v2.00a5LM 64-bit Intel (23 Sep 2023) www.cog-genomics.org/plink/2.0/ -(C) 2005-2023 Shaun Purcell, Christopher Chang GNU General Public License v3 -Logging to /scratch/prj/oliverpainfel/tmp/RtmpLV5vhT/profiles.chr22.log. +During startup - Warning messages: +1: Setting LC_COLLATE failed, using "C" +2: Setting LC_TIME failed, using "C" +3: Setting LC_MESSAGES failed, using "C" +4: Setting LC_MONETARY failed, using "C" +5: Setting LC_PAPER failed, using "C" +6: Setting LC_MEASUREMENT failed, using "C" +PLINK v2.00a5.12LM 64-bit Intel (25 Jun 2024) www.cog-genomics.org/plink/2.0/ +(C) 2005-2024 Shaun Purcell, Christopher Chang GNU General Public License v3 +Logging to /scratch/prj/oliverpainfel/tmp/RtmpZbyvBu/profiles.chr22.log. Options in effect: --chr 22 --keep misc/dev/test_data/output/example_plink2/ancestry/keep_files/model_based/EUR.keep - --out /scratch/prj/oliverpainfel/tmp/RtmpLV5vhT/profiles.chr22 + --out /scratch/prj/oliverpainfel/tmp/RtmpZbyvBu/profiles.chr22 --pfile misc/dev/test_data/output/example_plink2/geno/example_plink2.ref.chr22 --read-freq misc/dev/test_data/ref/freq_files/EUR/ref.EUR.chr22.afreq --score misc/dev/test_data/output/resources/data/ref/pc_score_files/EUR/ref-EUR-pcs.eigenvec.var.gz header-read cols=+scoresums,-scoreavgs --score-col-nums 4-9 --threads 1 -Start time: Thu Jul 25 09:41:00 2024 -1031702 MiB RAM detected, ~1018923 available; reserving 515851 MiB for main +Start time: Thu Jul 25 15:07:21 2024 +1031702 MiB RAM detected, ~1018589 available; reserving 515851 MiB for main workspace. Using 1 compute thread. 12 samples (5 females, 7 males; 12 founders) loaded from @@ -26,5 +33,5 @@ Note: No phenotype data present. --read-freq: Frequencies for 1000 variants loaded. --score: 144 variants processed. --score: Results written to -/scratch/prj/oliverpainfel/tmp/RtmpLV5vhT/profiles.chr22.sscore . -End time: Thu Jul 25 09:41:00 2024 +/scratch/prj/oliverpainfel/tmp/RtmpZbyvBu/profiles.chr22.sscore . +End time: Thu Jul 25 15:07:21 2024 diff --git a/pipeline/misc/dev/test_data/output/reference/logs/prep_pgs_lassosum_i-BODY04.log b/pipeline/misc/dev/test_data/output/reference/logs/prep_pgs_lassosum_i-BODY04.log index 9f6bc20..82a4020 100644 --- a/pipeline/misc/dev/test_data/output/reference/logs/prep_pgs_lassosum_i-BODY04.log +++ b/pipeline/misc/dev/test_data/output/reference/logs/prep_pgs_lassosum_i-BODY04.log @@ -1,17 +1,31 @@ -PLINK v2.00a5LM 64-bit Intel (23 Sep 2023) www.cog-genomics.org/plink/2.0/ -(C) 2005-2023 Shaun Purcell, Christopher Chang GNU General Public License v3 -Logging to /scratch/prj/oliverpainfel/tmp/Rtmpc9wErl/ref_merge.log. +During startup - Warning messages: +1: Setting LC_COLLATE failed, using "C" +2: Setting LC_TIME failed, using "C" +3: Setting LC_MESSAGES failed, using "C" +4: Setting LC_MONETARY failed, using "C" +5: Setting LC_PAPER failed, using "C" +6: Setting LC_MEASUREMENT failed, using "C" +During startup - Warning messages: +1: Setting LC_COLLATE failed, using "C" +2: Setting LC_TIME failed, using "C" +3: Setting LC_MESSAGES failed, using "C" +4: Setting LC_MONETARY failed, using "C" +5: Setting LC_PAPER failed, using "C" +6: Setting LC_MEASUREMENT failed, using "C" +PLINK v2.00a5.12LM 64-bit Intel (25 Jun 2024) www.cog-genomics.org/plink/2.0/ +(C) 2005-2024 Shaun Purcell, Christopher Chang GNU General Public License v3 +Logging to /scratch/prj/oliverpainfel/tmp/RtmpxaNyi5/ref_merge.log. Options in effect: - --extract /scratch/prj/oliverpainfel/tmp/Rtmpc9wErl/extract.snplist + --extract /scratch/prj/oliverpainfel/tmp/RtmpxaNyi5/extract.snplist --keep misc/dev/test_data/ref/keep_files/EUR.keep --make-bed --memory 4000 - --out /scratch/prj/oliverpainfel/tmp/Rtmpc9wErl/ref_merge + --out /scratch/prj/oliverpainfel/tmp/RtmpxaNyi5/ref_merge --pfile misc/dev/test_data/ref/ref.chr22 --threads 1 -Start time: Thu Jul 25 10:18:30 2024 -1031702 MiB RAM detected, ~1018764 available; reserving 4000 MiB for main +Start time: Thu Jul 25 15:07:04 2024 +1031702 MiB RAM detected, ~1018391 available; reserving 4000 MiB for main workspace. Using 1 compute thread. 3313 samples (1568 females, 1745 males; 3313 founders) loaded from @@ -23,10 +37,10 @@ misc/dev/test_data/ref/ref.chr22.psam. 665 samples (335 females, 330 males; 665 founders) remaining after main filters. 841 variants remaining after main filters. -Writing /scratch/prj/oliverpainfel/tmp/Rtmpc9wErl/ref_merge.fam ... done. -Writing /scratch/prj/oliverpainfel/tmp/Rtmpc9wErl/ref_merge.bim ... done. -Writing /scratch/prj/oliverpainfel/tmp/Rtmpc9wErl/ref_merge.bed ... 0%done. -End time: Thu Jul 25 10:18:30 2024 +Writing /scratch/prj/oliverpainfel/tmp/RtmpxaNyi5/ref_merge.fam ... done. +Writing /scratch/prj/oliverpainfel/tmp/RtmpxaNyi5/ref_merge.bim ... done. +Writing /scratch/prj/oliverpainfel/tmp/RtmpxaNyi5/ref_merge.bed ... 0%done. +End time: Thu Jul 25 15:07:04 2024 Coordinating summary stats with reference panel... Splitting genome by LD blocks ... Running lassosum ... @@ -42,19 +56,19 @@ Step 3... compute p-values and estimate empirical PDF/CDF Step 4... compute q-values and local fdr Performing pseudovalidation ... -PLINK v2.00a5LM 64-bit Intel (23 Sep 2023) www.cog-genomics.org/plink/2.0/ -(C) 2005-2023 Shaun Purcell, Christopher Chang GNU General Public License v3 -Logging to /scratch/prj/oliverpainfel/tmp/Rtmpc9wErl/profiles.chr22.log. +PLINK v2.00a5.12LM 64-bit Intel (25 Jun 2024) www.cog-genomics.org/plink/2.0/ +(C) 2005-2024 Shaun Purcell, Christopher Chang GNU General Public License v3 +Logging to /scratch/prj/oliverpainfel/tmp/RtmpxaNyi5/profiles.chr22.log. Options in effect: --chr 22 - --out /scratch/prj/oliverpainfel/tmp/Rtmpc9wErl/profiles.chr22 + --out /scratch/prj/oliverpainfel/tmp/RtmpxaNyi5/profiles.chr22 --pfile misc/dev/test_data/ref/ref.chr22 --score misc/dev/test_data/output/reference/pgs_score_files/lassosum/BODY04/ref-BODY04.score.gz header-read no-mean-imputation cols=+scoresums,-scoreavgs --score-col-nums 4-83 --threads 1 -Start time: Thu Jul 25 10:18:54 2024 -1031702 MiB RAM detected, ~1018728 available; reserving 515851 MiB for main +Start time: Thu Jul 25 15:07:05 2024 +1031702 MiB RAM detected, ~1018353 available; reserving 515851 MiB for main workspace. Using 1 compute thread. 3313 samples (1568 females, 1745 males; 3313 founders) loaded from @@ -63,5 +77,5 @@ misc/dev/test_data/ref/ref.chr22.psam. 3 categorical phenotypes loaded. --score: 1000 variants processed. --score: Results written to -/scratch/prj/oliverpainfel/tmp/Rtmpc9wErl/profiles.chr22.sscore . -End time: Thu Jul 25 10:18:54 2024 +/scratch/prj/oliverpainfel/tmp/RtmpxaNyi5/profiles.chr22.sscore . +End time: Thu Jul 25 15:07:05 2024 diff --git a/pipeline/misc/dev/test_data/output/reference/logs/prep_pgs_ptclump_i-BODY04.log b/pipeline/misc/dev/test_data/output/reference/logs/prep_pgs_ptclump_i-BODY04.log index 02ba910..50d4821 100644 --- a/pipeline/misc/dev/test_data/output/reference/logs/prep_pgs_ptclump_i-BODY04.log +++ b/pipeline/misc/dev/test_data/output/reference/logs/prep_pgs_ptclump_i-BODY04.log @@ -1,22 +1,29 @@ +During startup - Warning messages: +1: Setting LC_COLLATE failed, using "C" +2: Setting LC_TIME failed, using "C" +3: Setting LC_MESSAGES failed, using "C" +4: Setting LC_MONETARY failed, using "C" +5: Setting LC_PAPER failed, using "C" +6: Setting LC_MEASUREMENT failed, using "C" Warning message: In min(hla$P) : no non-missing arguments to min; returning Inf -PLINK v2.00a5LM 64-bit Intel (23 Sep 2023) www.cog-genomics.org/plink/2.0/ -(C) 2005-2023 Shaun Purcell, Christopher Chang GNU General Public License v3 -Logging to /scratch/prj/oliverpainfel/tmp/RtmpUDOb4s/file2003c62cca9ee1.chr22.log. +PLINK v2.00a5.12LM 64-bit Intel (25 Jun 2024) www.cog-genomics.org/plink/2.0/ +(C) 2005-2024 Shaun Purcell, Christopher Chang GNU General Public License v3 +Logging to /scratch/prj/oliverpainfel/tmp/RtmpRtlMvU/filedbed7992b197.chr22.log. Options in effect: - --clump /scratch/prj/oliverpainfel/tmp/RtmpUDOb4s/file2003c63759f286 + --clump /scratch/prj/oliverpainfel/tmp/RtmpRtlMvU/filedbed1853232e --clump-kb 250 --clump-p1 1 --clump-p2 1 --clump-r2 0.1 --keep misc/dev/test_data/ref/keep_files/EUR.keep --memory 4000 - --out /scratch/prj/oliverpainfel/tmp/RtmpUDOb4s/file2003c62cca9ee1.chr22 + --out /scratch/prj/oliverpainfel/tmp/RtmpRtlMvU/filedbed7992b197.chr22 --pfile misc/dev/test_data/ref/ref.chr22 --threads 1 -Start time: Thu Jun 6 14:44:53 2024 -1031702 MiB RAM detected, ~1016559 available; reserving 4000 MiB for main +Start time: Thu Jul 25 15:07:23 2024 +1031702 MiB RAM detected, ~1018588 available; reserving 4000 MiB for main workspace. Using 1 compute thread. 3313 samples (1568 females, 1745 males; 3313 founders) loaded from @@ -27,21 +34,21 @@ misc/dev/test_data/ref/ref.chr22.psam. 665 samples (335 females, 330 males; 665 founders) remaining after main filters. --clump: 0/841 index candidates processed. --clump: 148 clumps formed from 841 index candidates. -Results written to /scratch/prj/oliverpainfel/tmp/RtmpUDOb4s/file2003c62cca9ee1.chr22.clumps . -End time: Thu Jun 6 14:44:53 2024 -PLINK v2.00a5LM 64-bit Intel (23 Sep 2023) www.cog-genomics.org/plink/2.0/ -(C) 2005-2023 Shaun Purcell, Christopher Chang GNU General Public License v3 -Logging to /scratch/prj/oliverpainfel/tmp/RtmpUDOb4s/profiles.chr22.log. +Results written to /scratch/prj/oliverpainfel/tmp/RtmpRtlMvU/filedbed7992b197.chr22.clumps . +End time: Thu Jul 25 15:07:23 2024 +PLINK v2.00a5.12LM 64-bit Intel (25 Jun 2024) www.cog-genomics.org/plink/2.0/ +(C) 2005-2024 Shaun Purcell, Christopher Chang GNU General Public License v3 +Logging to /scratch/prj/oliverpainfel/tmp/RtmpRtlMvU/profiles.chr22.log. Options in effect: --chr 22 - --out /scratch/prj/oliverpainfel/tmp/RtmpUDOb4s/profiles.chr22 + --out /scratch/prj/oliverpainfel/tmp/RtmpRtlMvU/profiles.chr22 --pfile misc/dev/test_data/ref/ref.chr22 --score misc/dev/test_data/output/reference/pgs_score_files/ptclump/BODY04/ref-BODY04.score.gz header-read no-mean-imputation cols=+scoresums,-scoreavgs --score-col-nums 4-9 --threads 1 -Start time: Thu Jun 6 14:44:53 2024 -1031702 MiB RAM detected, ~1016553 available; reserving 515851 MiB for main +Start time: Thu Jul 25 15:07:23 2024 +1031702 MiB RAM detected, ~1018583 available; reserving 515851 MiB for main workspace. Using 1 compute thread. 3313 samples (1568 females, 1745 males; 3313 founders) loaded from @@ -50,5 +57,5 @@ misc/dev/test_data/ref/ref.chr22.psam. 3 categorical phenotypes loaded. --score: 1000 variants processed. --score: Results written to -/scratch/prj/oliverpainfel/tmp/RtmpUDOb4s/profiles.chr22.sscore . -End time: Thu Jun 6 14:44:53 2024 +/scratch/prj/oliverpainfel/tmp/RtmpRtlMvU/profiles.chr22.sscore . +End time: Thu Jul 25 15:07:23 2024 diff --git a/pipeline/misc/dev/test_data/output/reference/logs/sample_report_i-example_plink2.log b/pipeline/misc/dev/test_data/output/reference/logs/sample_report_i-example_plink2.log index 21b3453..62dffe9 100644 --- a/pipeline/misc/dev/test_data/output/reference/logs/sample_report_i-example_plink2.log +++ b/pipeline/misc/dev/test_data/output/reference/logs/sample_report_i-example_plink2.log @@ -1,3 +1,10 @@ +During startup - Warning messages: +1: Setting LC_COLLATE failed, using "C" +2: Setting LC_TIME failed, using "C" +3: Setting LC_MESSAGES failed, using "C" +4: Setting LC_MONETARY failed, using "C" +5: Setting LC_PAPER failed, using "C" +6: Setting LC_MEASUREMENT failed, using "C" processing file: samp_report_creator.Rmd @@ -26,6 +33,6 @@ processing file: samp_report_creator.Rmd 23/23 output file: samp_report_creator.knit.md -/scratch/prj/oliverpainfel/Software/MyGit/GenoPred/pipeline/.snakemake/conda/aea4ef260655c3bcc12fec8909f5f6dd_/bin/pandoc +RTS -K512m -RTS samp_report_creator.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /scratch/prj/oliverpainfel/Software/MyGit/GenoPred/pipeline/misc/dev/test_data/output/example_plink2/reports/example_plink2-report.html --lua-filter /scratch/prj/oliverpainfel/Software/MyGit/GenoPred/pipeline/.snakemake/conda/aea4ef260655c3bcc12fec8909f5f6dd_/lib/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /scratch/prj/oliverpainfel/Software/MyGit/GenoPred/pipeline/.snakemake/conda/aea4ef260655c3bcc12fec8909f5f6dd_/lib/R/library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /scratch/prj/oliverpainfel/Software/MyGit/GenoPred/pipeline/.snakemake/conda/aea4ef260655c3bcc12fec8909f5f6dd_/lib/R/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=cosmo --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /scratch/prj/oliverpainfel/tmp/Rtmppu1dQp/rmarkdown-stra498ff1043a.html +/tools/GenoPred/pipeline/.snakemake/conda/4e4fa1f1bb8db14f9a36511ee76ae12c_/bin/pandoc +RTS -K512m -RTS samp_report_creator.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tools/GenoPred/pipeline/misc/dev/test_data/output/example_plink2/reports/example_plink2-report.html --lua-filter /tools/GenoPred/pipeline/.snakemake/conda/4e4fa1f1bb8db14f9a36511ee76ae12c_/lib/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /tools/GenoPred/pipeline/.snakemake/conda/4e4fa1f1bb8db14f9a36511ee76ae12c_/lib/R/library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /tools/GenoPred/pipeline/.snakemake/conda/4e4fa1f1bb8db14f9a36511ee76ae12c_/lib/R/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=cosmo --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /scratch/prj/oliverpainfel/tmp/RtmplgMePK/rmarkdown-strddc05515350b.html Output created: misc/dev/test_data/output/example_plink2/reports/example_plink2-report.html diff --git a/pipeline/misc/dev/test_data/output/reference/logs/score_reporter.log b/pipeline/misc/dev/test_data/output/reference/logs/score_reporter.log index 0855139..9c7a987 100644 --- a/pipeline/misc/dev/test_data/output/reference/logs/score_reporter.log +++ b/pipeline/misc/dev/test_data/output/reference/logs/score_reporter.log @@ -1 +1,8 @@ +During startup - Warning messages: +1: Setting LC_COLLATE failed, using "C" +2: Setting LC_TIME failed, using "C" +3: Setting LC_MESSAGES failed, using "C" +4: Setting LC_MONETARY failed, using "C" +5: Setting LC_PAPER failed, using "C" +6: Setting LC_MEASUREMENT failed, using "C" [1] "misc/dev/test_data/output" diff --git a/pipeline/misc/dev/test_data/output/reference/logs/sumstat_prep_i-BODY04.log b/pipeline/misc/dev/test_data/output/reference/logs/sumstat_prep_i-BODY04.log index e69de29..46b320d 100644 --- a/pipeline/misc/dev/test_data/output/reference/logs/sumstat_prep_i-BODY04.log +++ b/pipeline/misc/dev/test_data/output/reference/logs/sumstat_prep_i-BODY04.log @@ -0,0 +1,7 @@ +During startup - Warning messages: +1: Setting LC_COLLATE failed, using "C" +2: Setting LC_TIME failed, using "C" +3: Setting LC_MESSAGES failed, using "C" +4: Setting LC_MONETARY failed, using "C" +5: Setting LC_PAPER failed, using "C" +6: Setting LC_MEASUREMENT failed, using "C" diff --git a/pipeline/misc/dev/test_data/output/reference/logs/target_pgs_i-example_plink2-AFR.log b/pipeline/misc/dev/test_data/output/reference/logs/target_pgs_i-example_plink2-AFR.log index 242c58d..bd8fa1d 100644 --- a/pipeline/misc/dev/test_data/output/reference/logs/target_pgs_i-example_plink2-AFR.log +++ b/pipeline/misc/dev/test_data/output/reference/logs/target_pgs_i-example_plink2-AFR.log @@ -1,22 +1,29 @@ +During startup - Warning messages: +1: Setting LC_COLLATE failed, using "C" +2: Setting LC_TIME failed, using "C" +3: Setting LC_MESSAGES failed, using "C" +4: Setting LC_MONETARY failed, using "C" +5: Setting LC_PAPER failed, using "C" +6: Setting LC_MEASUREMENT failed, using "C" Loading required package: iterators Loading required package: parallel [1] 0 0 0 [1] 0 -PLINK v2.00a5LM 64-bit Intel (23 Sep 2023) www.cog-genomics.org/plink/2.0/ -(C) 2005-2023 Shaun Purcell, Christopher Chang GNU General Public License v3 -Logging to /scratch/prj/oliverpainfel/tmp/RtmpJojrU9/profiles.chr22.log. +PLINK v2.00a5.12LM 64-bit Intel (25 Jun 2024) www.cog-genomics.org/plink/2.0/ +(C) 2005-2024 Shaun Purcell, Christopher Chang GNU General Public License v3 +Logging to /scratch/prj/oliverpainfel/tmp/RtmpUg6RoM/profiles.chr22.log. Options in effect: --chr 22 --keep misc/dev/test_data/output/example_plink2/ancestry/keep_files/model_based/AFR.keep - --out /scratch/prj/oliverpainfel/tmp/RtmpJojrU9/profiles.chr22 + --out /scratch/prj/oliverpainfel/tmp/RtmpUg6RoM/profiles.chr22 --pfile misc/dev/test_data/output/example_plink2/geno/example_plink2.ref.chr22 --read-freq misc/dev/test_data/ref/freq_files/AFR/ref.AFR.chr22.afreq - --score /scratch/prj/oliverpainfel/tmp/RtmpJojrU9/all_score.txt header-read cols=+scoresums,-scoreavgs + --score /scratch/prj/oliverpainfel/tmp/RtmpUg6RoM/all_score.txt header-read cols=+scoresums,-scoreavgs --score-col-nums 4-90 --threads 1 -Start time: Thu Jul 25 11:37:16 2024 -1031702 MiB RAM detected, ~1018655 available; reserving 515851 MiB for main +Start time: Thu Jul 25 15:07:25 2024 +1031702 MiB RAM detected, ~1018585 available; reserving 515851 MiB for main workspace. Using 1 compute thread. 12 samples (5 females, 7 males; 12 founders) loaded from @@ -30,5 +37,5 @@ Note: No phenotype data present. --read-freq: Frequencies for 1000 variants loaded. --score: 1000 variants processed. --score: Results written to -/scratch/prj/oliverpainfel/tmp/RtmpJojrU9/profiles.chr22.sscore . -End time: Thu Jul 25 11:37:16 2024 +/scratch/prj/oliverpainfel/tmp/RtmpUg6RoM/profiles.chr22.sscore . +End time: Thu Jul 25 15:07:25 2024 diff --git a/pipeline/misc/dev/test_data/output/reference/logs/target_pgs_i-example_plink2-CSA.log b/pipeline/misc/dev/test_data/output/reference/logs/target_pgs_i-example_plink2-CSA.log index 09caaaf..1a92b40 100644 --- a/pipeline/misc/dev/test_data/output/reference/logs/target_pgs_i-example_plink2-CSA.log +++ b/pipeline/misc/dev/test_data/output/reference/logs/target_pgs_i-example_plink2-CSA.log @@ -1,22 +1,29 @@ +During startup - Warning messages: +1: Setting LC_COLLATE failed, using "C" +2: Setting LC_TIME failed, using "C" +3: Setting LC_MESSAGES failed, using "C" +4: Setting LC_MONETARY failed, using "C" +5: Setting LC_PAPER failed, using "C" +6: Setting LC_MEASUREMENT failed, using "C" Loading required package: iterators Loading required package: parallel [1] 0 0 0 [1] 0 -PLINK v2.00a5LM 64-bit Intel (23 Sep 2023) www.cog-genomics.org/plink/2.0/ -(C) 2005-2023 Shaun Purcell, Christopher Chang GNU General Public License v3 -Logging to /scratch/prj/oliverpainfel/tmp/RtmpJ3GZLi/profiles.chr22.log. +PLINK v2.00a5.12LM 64-bit Intel (25 Jun 2024) www.cog-genomics.org/plink/2.0/ +(C) 2005-2024 Shaun Purcell, Christopher Chang GNU General Public License v3 +Logging to /scratch/prj/oliverpainfel/tmp/Rtmp8caZmr/profiles.chr22.log. Options in effect: --chr 22 --keep misc/dev/test_data/output/example_plink2/ancestry/keep_files/model_based/CSA.keep - --out /scratch/prj/oliverpainfel/tmp/RtmpJ3GZLi/profiles.chr22 + --out /scratch/prj/oliverpainfel/tmp/Rtmp8caZmr/profiles.chr22 --pfile misc/dev/test_data/output/example_plink2/geno/example_plink2.ref.chr22 --read-freq misc/dev/test_data/ref/freq_files/CSA/ref.CSA.chr22.afreq - --score /scratch/prj/oliverpainfel/tmp/RtmpJ3GZLi/all_score.txt header-read cols=+scoresums,-scoreavgs + --score /scratch/prj/oliverpainfel/tmp/Rtmp8caZmr/all_score.txt header-read cols=+scoresums,-scoreavgs --score-col-nums 4-90 --threads 1 -Start time: Thu Jul 25 11:37:17 2024 -1031702 MiB RAM detected, ~1018655 available; reserving 515851 MiB for main +Start time: Thu Jul 25 15:07:26 2024 +1031702 MiB RAM detected, ~1018585 available; reserving 515851 MiB for main workspace. Using 1 compute thread. 12 samples (5 females, 7 males; 12 founders) loaded from @@ -30,5 +37,5 @@ Note: No phenotype data present. --read-freq: Frequencies for 1000 variants loaded. --score: 1000 variants processed. --score: Results written to -/scratch/prj/oliverpainfel/tmp/RtmpJ3GZLi/profiles.chr22.sscore . -End time: Thu Jul 25 11:37:17 2024 +/scratch/prj/oliverpainfel/tmp/Rtmp8caZmr/profiles.chr22.sscore . +End time: Thu Jul 25 15:07:26 2024 diff --git a/pipeline/misc/dev/test_data/output/reference/logs/target_pgs_i-example_plink2-EAS.log b/pipeline/misc/dev/test_data/output/reference/logs/target_pgs_i-example_plink2-EAS.log index 63af772..0945cdb 100644 --- a/pipeline/misc/dev/test_data/output/reference/logs/target_pgs_i-example_plink2-EAS.log +++ b/pipeline/misc/dev/test_data/output/reference/logs/target_pgs_i-example_plink2-EAS.log @@ -1,22 +1,29 @@ +During startup - Warning messages: +1: Setting LC_COLLATE failed, using "C" +2: Setting LC_TIME failed, using "C" +3: Setting LC_MESSAGES failed, using "C" +4: Setting LC_MONETARY failed, using "C" +5: Setting LC_PAPER failed, using "C" +6: Setting LC_MEASUREMENT failed, using "C" Loading required package: iterators Loading required package: parallel [1] 0 0 0 [1] 0 -PLINK v2.00a5LM 64-bit Intel (23 Sep 2023) www.cog-genomics.org/plink/2.0/ -(C) 2005-2023 Shaun Purcell, Christopher Chang GNU General Public License v3 -Logging to /scratch/prj/oliverpainfel/tmp/Rtmpp21G7i/profiles.chr22.log. +PLINK v2.00a5.12LM 64-bit Intel (25 Jun 2024) www.cog-genomics.org/plink/2.0/ +(C) 2005-2024 Shaun Purcell, Christopher Chang GNU General Public License v3 +Logging to /scratch/prj/oliverpainfel/tmp/Rtmp5iYRxD/profiles.chr22.log. Options in effect: --chr 22 --keep misc/dev/test_data/output/example_plink2/ancestry/keep_files/model_based/EAS.keep - --out /scratch/prj/oliverpainfel/tmp/Rtmpp21G7i/profiles.chr22 + --out /scratch/prj/oliverpainfel/tmp/Rtmp5iYRxD/profiles.chr22 --pfile misc/dev/test_data/output/example_plink2/geno/example_plink2.ref.chr22 --read-freq misc/dev/test_data/ref/freq_files/EAS/ref.EAS.chr22.afreq - --score /scratch/prj/oliverpainfel/tmp/Rtmpp21G7i/all_score.txt header-read cols=+scoresums,-scoreavgs + --score /scratch/prj/oliverpainfel/tmp/Rtmp5iYRxD/all_score.txt header-read cols=+scoresums,-scoreavgs --score-col-nums 4-90 --threads 1 -Start time: Thu Jul 25 11:37:15 2024 -1031702 MiB RAM detected, ~1018655 available; reserving 515851 MiB for main +Start time: Thu Jul 25 15:07:25 2024 +1031702 MiB RAM detected, ~1018587 available; reserving 515851 MiB for main workspace. Using 1 compute thread. 12 samples (5 females, 7 males; 12 founders) loaded from @@ -30,5 +37,5 @@ Note: No phenotype data present. --read-freq: Frequencies for 1000 variants loaded. --score: 1000 variants processed. --score: Results written to -/scratch/prj/oliverpainfel/tmp/Rtmpp21G7i/profiles.chr22.sscore . -End time: Thu Jul 25 11:37:15 2024 +/scratch/prj/oliverpainfel/tmp/Rtmp5iYRxD/profiles.chr22.sscore . +End time: Thu Jul 25 15:07:25 2024 diff --git a/pipeline/misc/dev/test_data/output/reference/logs/target_pgs_i-example_plink2-EUR.log b/pipeline/misc/dev/test_data/output/reference/logs/target_pgs_i-example_plink2-EUR.log index 3e58494..8149054 100644 --- a/pipeline/misc/dev/test_data/output/reference/logs/target_pgs_i-example_plink2-EUR.log +++ b/pipeline/misc/dev/test_data/output/reference/logs/target_pgs_i-example_plink2-EUR.log @@ -1,22 +1,29 @@ +During startup - Warning messages: +1: Setting LC_COLLATE failed, using "C" +2: Setting LC_TIME failed, using "C" +3: Setting LC_MESSAGES failed, using "C" +4: Setting LC_MONETARY failed, using "C" +5: Setting LC_PAPER failed, using "C" +6: Setting LC_MEASUREMENT failed, using "C" Loading required package: iterators Loading required package: parallel [1] 0 0 0 [1] 0 -PLINK v2.00a5LM 64-bit Intel (23 Sep 2023) www.cog-genomics.org/plink/2.0/ -(C) 2005-2023 Shaun Purcell, Christopher Chang GNU General Public License v3 -Logging to /scratch/prj/oliverpainfel/tmp/RtmpnTRJEO/profiles.chr22.log. +PLINK v2.00a5.12LM 64-bit Intel (25 Jun 2024) www.cog-genomics.org/plink/2.0/ +(C) 2005-2024 Shaun Purcell, Christopher Chang GNU General Public License v3 +Logging to /scratch/prj/oliverpainfel/tmp/RtmpK7LCqC/profiles.chr22.log. Options in effect: --chr 22 --keep misc/dev/test_data/output/example_plink2/ancestry/keep_files/model_based/EUR.keep - --out /scratch/prj/oliverpainfel/tmp/RtmpnTRJEO/profiles.chr22 + --out /scratch/prj/oliverpainfel/tmp/RtmpK7LCqC/profiles.chr22 --pfile misc/dev/test_data/output/example_plink2/geno/example_plink2.ref.chr22 --read-freq misc/dev/test_data/ref/freq_files/EUR/ref.EUR.chr22.afreq - --score /scratch/prj/oliverpainfel/tmp/RtmpnTRJEO/all_score.txt header-read cols=+scoresums,-scoreavgs + --score /scratch/prj/oliverpainfel/tmp/RtmpK7LCqC/all_score.txt header-read cols=+scoresums,-scoreavgs --score-col-nums 4-90 --threads 1 -Start time: Thu Jul 25 11:37:15 2024 -1031702 MiB RAM detected, ~1018655 available; reserving 515851 MiB for main +Start time: Thu Jul 25 15:07:24 2024 +1031702 MiB RAM detected, ~1018587 available; reserving 515851 MiB for main workspace. Using 1 compute thread. 12 samples (5 females, 7 males; 12 founders) loaded from @@ -30,5 +37,5 @@ Note: No phenotype data present. --read-freq: Frequencies for 1000 variants loaded. --score: 1000 variants processed. --score: Results written to -/scratch/prj/oliverpainfel/tmp/RtmpnTRJEO/profiles.chr22.sscore . -End time: Thu Jul 25 11:37:15 2024 +/scratch/prj/oliverpainfel/tmp/RtmpK7LCqC/profiles.chr22.sscore . +End time: Thu Jul 25 15:07:24 2024 diff --git a/pipeline/misc/dev/test_data/output/reference/pgs_score_files/lassosum/BODY04/ref-BODY04.log b/pipeline/misc/dev/test_data/output/reference/pgs_score_files/lassosum/BODY04/ref-BODY04.log index 423d7d7..b81d89a 100644 --- a/pipeline/misc/dev/test_data/output/reference/pgs_score_files/lassosum/BODY04/ref-BODY04.log +++ b/pipeline/misc/dev/test_data/output/reference/pgs_score_files/lassosum/BODY04/ref-BODY04.log @@ -3,7 +3,7 @@ # For questions contact Oliver Pain (oliver.pain@kcl.ac.uk) ################################################################# # Repository: GenoPred -# Version (tag): v2.2.2-95-g19dbe57 +# Version (tag): v2.2.2-102-g0438efa --------------- Parameter Value ref_plink_chr misc/dev/test_data/ref/ref.chr @@ -18,21 +18,21 @@ help FALSE output_dir misc/dev/test_data/output/reference/pgs_score_files/lassosum/BODY04/ --------------- -Analysis started at 2024-07-25 10:18:27 +Analysis started at 2024-07-25 15:07:02 Reading in GWAS. sumstats contains 841 variants. 841 variants remain after selecting chromosomes. sumstats contains 841 variants with complete data. Merging per chromosome reference data. -Test started at 2024-07-25 10:18:30 +Test started at 2024-07-25 15:07:04 Running lassosum pipeline. Performing pseudovalidation. Pseudovalidated parameters: s = 0.2 lambda = 0.001 value = 0 -Test run finished at 2024-07-25 10:18:53 -Test duration was 22.83 secs +Test run finished at 2024-07-25 15:07:05 +Test duration was 0.48 secs Calculating polygenic scores in reference. -Analysis finished at 2024-07-25 10:18:54 -Analysis duration was 26.84 secs +Analysis finished at 2024-07-25 15:07:05 +Analysis duration was 2.79 secs diff --git a/pipeline/misc/dev/test_data/output/reference/pgs_score_files/lassosum/BODY04/ref-BODY04.score.gz b/pipeline/misc/dev/test_data/output/reference/pgs_score_files/lassosum/BODY04/ref-BODY04.score.gz index 91b8cf3..0f2f86d 100644 Binary files a/pipeline/misc/dev/test_data/output/reference/pgs_score_files/lassosum/BODY04/ref-BODY04.score.gz and b/pipeline/misc/dev/test_data/output/reference/pgs_score_files/lassosum/BODY04/ref-BODY04.score.gz differ diff --git a/pipeline/misc/dev/test_data/output/reference/pgs_score_files/ptclump/BODY04/ref-BODY04.log b/pipeline/misc/dev/test_data/output/reference/pgs_score_files/ptclump/BODY04/ref-BODY04.log index 0f17f9f..6698dc3 100644 --- a/pipeline/misc/dev/test_data/output/reference/pgs_score_files/ptclump/BODY04/ref-BODY04.log +++ b/pipeline/misc/dev/test_data/output/reference/pgs_score_files/ptclump/BODY04/ref-BODY04.log @@ -3,7 +3,7 @@ # For questions contact Oliver Pain (oliver.pain@kcl.ac.uk) ################################################################# # Repository: GenoPred -# Version (tag): v2.2.2-51-g51c6c09 +# Version (tag): v2.2.2-102-g0438efa --------------- Parameter Value ref_plink_chr misc/dev/test_data/ref/ref.chr @@ -20,19 +20,19 @@ help FALSE output_dir misc/dev/test_data/output/reference/pgs_score_files/ptclump/BODY04/ --------------- -Analysis started at 2024-06-06 14:44:53 +Analysis started at 2024-07-25 15:07:23 Reading in GWAS. sumstats contains 841 variants. 841 variants remain after selecting chromosomes. sumstats contains 841 variants with complete data. Extracted top variant in HLA/MHC region. 841 variants remain. -Test started at 2024-06-06 14:44:53 +Test started at 2024-07-25 15:07:23 Performing LD-based clumping. 148 variants remain after clumping. Creating score file. -Test run finished at 2024-06-06 14:44:53 -Test duration was 0.08 secs +Test run finished at 2024-07-25 15:07:23 +Test duration was 0.1 secs Calculating polygenic scores in reference. -Analysis finished at 2024-06-06 14:44:53 -Analysis duration was 0.47 secs +Analysis finished at 2024-07-25 15:07:23 +Analysis duration was 0.74 secs diff --git a/pipeline/misc/dev/test_data/output/reference/pgs_score_files/ptclump/BODY04/ref-BODY04.score.gz b/pipeline/misc/dev/test_data/output/reference/pgs_score_files/ptclump/BODY04/ref-BODY04.score.gz index 797e653..17c32c2 100644 Binary files a/pipeline/misc/dev/test_data/output/reference/pgs_score_files/ptclump/BODY04/ref-BODY04.score.gz and b/pipeline/misc/dev/test_data/output/reference/pgs_score_files/ptclump/BODY04/ref-BODY04.score.gz differ diff --git a/pipeline/misc/dev/test_setup.Rmd b/pipeline/misc/dev/test_setup.Rmd index 564daf6..8019aa6 100644 --- a/pipeline/misc/dev/test_setup.Rmd +++ b/pipeline/misc/dev/test_setup.Rmd @@ -159,16 +159,33 @@ write.table(config, 'misc/dev/test_data/config/config.yaml', col.names = F, row. ## Run pipeline +Generate the reference data within the latest GenoPred container to ensure perfect reproduction. + ```{bash} -cd /users/k1806347/oliverpainfel/Software/MyGit/GenoPred/pipeline + +singularity shell \ + --bind /scratch/prj/oliverpainfel:/scratch/prj/oliverpainfel \ + --writable-tmpfs \ + /users/k1806347/oliverpainfel/Software/singularity/genopred_pipeline_latest.sif + +# Activate env and pull latest version from dev +source /opt/mambaforge/etc/profile.d/conda.sh conda activate genopred +cd /tools/GenoPred/pipeline +git checkout dev +git pull + +# Run pipeline snakemake \ - -j1 \ - --use-conda \ - output_all \ - pc_projection \ - misc/dev/test_data/output/reference/target_checks/example_plink2/indiv_report-4_EAS.4_EAS-report.done \ - --configfile=misc/dev/test_data/config/config.yaml +-j1 \ +--use-conda \ +output_all \ +pc_projection \ +misc/dev/test_data/output/reference/target_checks/example_plink2/indiv_report-4_EAS.4_EAS-report.done \ +--configfile=misc/dev/test_data/config/config.yaml + +# Move output outside the container so it can be pushed to the repo +mv misc/dev/test_data/output /scratch/prj/oliverpainfel/Software/MyGit/GenoPred/pipeline/misc/dev/test_data/output ``` ***