DAY-EC activated.
DAY-EC activated.
            done
            for rel in $optional_rels; do
                link_or_copy_optional "$rel"
            done
        elif [ mounted = "s3" ]; then
            if [ -z s3://lsmc-ssf-sequencing-data/basecalls/lsmc/ssf-hq/LH01106/2026/20260514_LH01106_0009_B23TVLGLT4/ ]; then
                echo "SOURCE_S3_URI is required for Illumina run QC S3 mode" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/logs/metric_subset_fetched.log
                exit 2
            fi
            if [ -z lsmc ]; then
                echo "PROFILE is required for Illumina run QC S3 mode" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/logs/metric_subset_fetched.log
                exit 2
            fi
            if [ lsmc = "default" ]; then
                echo "PROFILE must not be default for Illumina run QC S3 mode" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/logs/metric_subset_fetched.log
                exit 2
            fi
            if [ -z us-west-2 ]; then
                echo "REGION is required for Illumina run QC S3 mode" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/logs/metric_subset_fetched.log
                exit 2
            fi
            command -v aws >> results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/logs/metric_subset_fetched.log 2>&1
            run_uri=$(printf "%s" s3://lsmc-ssf-sequencing-data/basecalls/lsmc/ssf-hq/LH01106/2026/20260514_LH01106_0009_B23TVLGLT4/ | sed 's:/*$::')
            for rel in $required_rels; do
                s3_copy_required "$rel"
            done
            for rel in $optional_rels; do
                s3_copy_optional "$rel"
            done
        else
            echo "Unsupported Illumina run QC mode: mounted" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/logs/metric_subset_fetched.log
            exit 2
        fi
        for rel in $required_rels; do
            test -s "results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/source_run_subset/$rel"
        done
        touch results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/logs/metric_subset_fetched.done

Activating conda environment: ../../../../resources/environments/conda/ubuntu/ip-10-0-0-88/a99ea18d415639f67a6e85afdbe2fe1b_
[Sat May 30 03:12:17 2026]
Finished job 3.
1 of 6 steps (17%) done
Select jobs to execute...

[Sat May 30 03:12:17 2026]
localrule illumina_run_qc_interop_summary:
    input: results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/logs/metric_subset_fetched.done
    output: results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/interop_summary.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/interop_index_summary.csv
    log: results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/logs/interop_summary.log
    jobid: 2
    benchmark: results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/benchmarks/interop_summary.bench.tsv
    reason: Missing output files: results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/interop_summary.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/interop_index_summary.csv; Input files updated by another job: results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/logs/metric_subset_fetched.done
    resources: mem_mb=3000, mem_mib=2862, disk_mb=1000, disk_mib=954, tmpdir=/dev/shm, threads=1, time=5440, partition=i192,i128,i192mem, vcpu=1, distribution=block, exclusive=, constraint=, exclude=, include=


        set -euo pipefail
        mkdir -p $(dirname results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/interop_summary.csv) $(dirname results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/logs/interop_summary.log)
        : > results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/logs/interop_summary.log
        test -d results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/source_run_subset/InterOp
        if [ -z "${CONDA_PREFIX:-}" ]; then
            echo "CONDA_PREFIX is required for illumina_run_qc_interop_summary" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/logs/interop_summary.log
            exit 2
        fi
        "$CONDA_PREFIX/bin/python" workflow/scripts/write_interop_summary_csv.py \
          --run-folder results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/source_run_subset \
          --summary-out results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/interop_summary.csv \
          --index-summary-out results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/interop_index_summary.csv \
          >> results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/logs/interop_summary.log 2>&1
        test -s results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/interop_summary.csv
        test -s results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/interop_index_summary.csv

Activating conda environment: ../../../../resources/environments/conda/ubuntu/ip-10-0-0-88/a99ea18d415639f67a6e85afdbe2fe1b_
[Sat May 30 03:12:29 2026]
Finished job 2.
2 of 6 steps (33%) done
Select jobs to execute...

[Sat May 30 03:12:29 2026]
localrule illumina_run_qc_json:
    input: results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/logs/metric_subset_fetched.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/interop_summary.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/interop_index_summary.csv
    output: results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/illumina_run_qc.json
    log: results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/logs/illumina_run_qc_json.log
    jobid: 4
    benchmark: results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/benchmarks/illumina_run_qc_json.bench.tsv
    reason: Missing output files: results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/illumina_run_qc.json; Input files updated by another job: results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/logs/metric_subset_fetched.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/interop_summary.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/interop_index_summary.csv
    resources: mem_mb=3000, mem_mib=2862, disk_mb=1000, disk_mib=954, tmpdir=/dev/shm, threads=1, time=5440, partition=i192,i128,i192mem, vcpu=1, distribution=block, exclusive=, constraint=, exclude=, include=


        set -euo pipefail
        mkdir -p $(dirname results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/illumina_run_qc.json) $(dirname results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/logs/illumina_run_qc_json.log)
        : > results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/logs/illumina_run_qc_json.log
        test -s results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/source_run_subset/RunInfo.xml
        if [ -z "${CONDA_PREFIX:-}" ]; then
            echo "CONDA_PREFIX is required for illumina_run_qc_json" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/logs/illumina_run_qc_json.log
            exit 2
        fi
        "$CONDA_PREFIX/bin/python" workflow/scripts/write_illumina_run_qc_json.py \
          --run-info results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/source_run_subset/RunInfo.xml \
          --interop-summary results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/interop_summary.csv \
          --interop-index-summary results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/interop_index_summary.csv \
          --output-json results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/illumina_run_qc.json \
          >> results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/logs/illumina_run_qc_json.log 2>&1
        python -m json.tool results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/illumina_run_qc.json > results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/illumina_run_qc.json.pretty
        mv results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/illumina_run_qc.json.pretty results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/illumina_run_qc.json

Activating conda environment: ../../../../resources/environments/conda/ubuntu/ip-10-0-0-88/a99ea18d415639f67a6e85afdbe2fe1b_
[Sat May 30 03:12:29 2026]
Finished job 4.
3 of 6 steps (50%) done
Select jobs to execute...

[Sat May 30 03:12:29 2026]
localrule illumina_run_qc_report:
    input: results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/interop_summary.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/interop_index_summary.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/illumina_run_qc.json
    output: results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/summary.html, results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/summary.tsv, results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/logs/illumina_run_qc_report.done
    log: results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/logs/illumina_run_qc_report.log
    jobid: 1
    benchmark: results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/benchmarks/illumina_run_qc_report.bench.tsv
    reason: Missing output files: results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/logs/illumina_run_qc_report.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/summary.html, results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/summary.tsv; Input files updated by another job: results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/illumina_run_qc.json, results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/interop_summary.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/interop_index_summary.csv
    resources: mem_mb=3000, mem_mib=2862, disk_mb=1000, disk_mib=954, tmpdir=/dev/shm, threads=1, time=5440, partition=i192,i128,i192mem, vcpu=1, distribution=block, exclusive=, constraint=, exclude=, include=


        set -euo pipefail
        mkdir -p $(dirname results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/summary.html) $(dirname results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/summary.tsv) $(dirname results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/logs/illumina_run_qc_report.log)
        python workflow/scripts/summarize_run_qc_report.py \
          --platform ILMN \
          --run-s3-uri s3://lsmc-ssf-sequencing-data/basecalls/lsmc/ssf-hq/LH01106/2026/20260514_LH01106_0009_B23TVLGLT4/ \
          --interop-summary results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/interop_summary.csv \
          --interop-index-summary results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/interop_index_summary.csv \
          --illumina-qc-json results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/illumina_run_qc.json \
          --output-html results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/summary.html \
          --output-tsv results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/summary.tsv \
          --done results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/logs/illumina_run_qc_report.done > results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/logs/illumina_run_qc_report.log 2>&1

Activating conda environment: ../../../../resources/environments/conda/ubuntu/ip-10-0-0-88/a99ea18d415639f67a6e85afdbe2fe1b_
[Sat May 30 03:12:30 2026]
Finished job 1.
4 of 6 steps (67%) done
Select jobs to execute...

[Sat May 30 03:12:30 2026]
localrule illumina_run_qc_multiqc:
    input: results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/interop_summary.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/interop_index_summary.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/illumina_run_qc.json, results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/summary.tsv, results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/logs/illumina_run_qc_report.done
    output: results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/multiqc_report.html, results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/multiqc_inputs/illumina_run_qc_summary_mqc.tsv, results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/multiqc_inputs/illumina_run_qc_multiqc_config.yaml
    log: results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/logs/illumina_run_qc_multiqc.log
    jobid: 5
    benchmark: results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/benchmarks/illumina_run_qc_multiqc.bench.tsv
    reason: Missing output files: results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/multiqc_report.html; Input files updated by another job: results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/illumina_run_qc.json, results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/logs/illumina_run_qc_report.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/summary.tsv, results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/interop_summary.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/interop_index_summary.csv
    resources: mem_mb=3000, mem_mib=2862, disk_mb=1000, disk_mib=954, tmpdir=/dev/shm, threads=1, time=5440, partition=i192,i128,i192mem, vcpu=1, distribution=block, exclusive=, constraint=, exclude=, include=


        set -euo pipefail
        mkdir -p $(dirname results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/multiqc_report.html) $(dirname results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/logs/illumina_run_qc_multiqc.log) results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/multiqc_inputs
        out=results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/multiqc_report.html
        multiqc --version > results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/logs/illumina_run_qc_multiqc.log 2>&1 || true
        python workflow/scripts/illumina_run_qc_to_multiqc.py \
          --summary-tsv results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/summary.tsv \
          --illumina-qc-json results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/illumina_run_qc.json \
          --summary-out results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/multiqc_inputs/illumina_run_qc_summary_mqc.tsv \
          --config-out results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/multiqc_inputs/illumina_run_qc_multiqc_config.yaml \
          >> results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/logs/illumina_run_qc_multiqc.log 2>&1
        multiqc -f \
          -m custom_content \
          --config results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/multiqc_inputs/illumina_run_qc_multiqc_config.yaml \
          --filename "$(basename "$out")" \
          --outdir "$(dirname "$out")" \
          results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/multiqc_inputs >> results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/logs/illumina_run_qc_multiqc.log 2>&1
        test -s results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/multiqc_report.html

Activating conda environment: ../../../../resources/environments/conda/ubuntu/ip-10-0-0-88/73dbbd9209dde9d5b560eca76639c2a0_
[Sat May 30 03:12:41 2026]
Finished job 5.
5 of 6 steps (83%) done
Select jobs to execute...

[Sat May 30 03:12:41 2026]
localrule produce_illumina_run_qc:
    input: results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/summary.html, results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/multiqc_report.html
    jobid: 0
    reason: Input files updated by another job: results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/summary.html, results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/multiqc_report.html
    resources: mem_mb=3000, mem_mib=2862, disk_mb=1000, disk_mib=954, tmpdir=/dev/shm, threads=1, time=5440, partition=i192,i128,i192mem, vcpu=1, distribution=block, exclusive=, constraint=, exclude=, include=

[Sat May 30 03:12:41 2026]
Finished job 0.
6 of 6 steps (100%) done
Complete log: .snakemake/log/2026-05-30T031212.197057.snakemake.log


	WARNING!!!! ALL Directories Are Remaining Unlocked. To have directories lock automatically upon successful completion, set --lock-analysis-dirs when calling day-run.



]]]]--------WORKFLOW SUCCESS====================]]]]]--
RETURN CODE: 0
⚠ Active conda environment is 'DAYOA', not DAY-EC. Continuing anyway; the
supported path is `source ./activate`.

── EXPORT ──
  › Preparing direct FSx export DRA
2026-05-30 03:12:49,247 INFO Found credentials from IAM Role: dyec-test-RoleHeadNode-eJMKI1vZVQBE
  · Attached export DRA dra-0907199c8677f6731 at
/fsx/analysis_results/ubuntu/ccv20260529r11_illumina_run_qc/
2026-05-30 03:15:23,917 INFO Task task-0e5c6d309148fa50b status: PENDING
2026-05-30 03:15:54,327 INFO Task task-0e5c6d309148fa50b status: EXECUTING
2026-05-30 03:16:24,546 INFO Task task-0e5c6d309148fa50b status: SUCCEEDED
2026-05-30 03:24:33,122 INFO Wrote export status to /home/ubuntu/daylily-runs/ccv20260529r11_illumina_run_qc/export/fsx_export.yaml

╭────────────────────────────── Export complete ───────────────────────────────╮
│                                                                              │
│  Cluster: dyec-test                                                          │
│  FSx: fs-0df313e1751219cac                                                   │
│  Source: /analysis_results/ubuntu/ccv20260529r11_illumina_run_qc/            │
│  S3:                                                                         │
│  s3://lsmc-ssf-sequencing-data/derived/validation/dyec-test/ubuntu/ccv20260  │
│  529r11_illumina_run_qc/                                                     │
│  Status file:                                                                │
│  /home/ubuntu/daylily-runs/ccv20260529r11_illumina_run_qc/export/fsx_export  │
│  .yaml                                                                       │
│                                                                              │
╰──────────────────────────────────────────────────────────────────────────────╯
[INFO] Deleted FSx analysis directory after successful export: /fsx/analysis_results/ubuntu/ccv20260529r11_illumina_run_qc
[INFO] Workflow exited with status 0
shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
ERROR: error getting working directory name: no such file or directory
      while executing
  "pwd"
      (procedure "getAbsolutePath" line 9)
      invoked from within
  "getAbsolutePath $::argv0"
      (procedure "cmdModuleAutoinit" line 19)
      invoked from within
  "cmdModuleAutoinit"
      (procedure "module" line 333)
      invoked from within
  "{*}$execcmdlist"
  Please report this issue at https://github.com/cea-hpc/modules/issues
chdir: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
DAY-EC activated.
✗ Unexpected error: [Errno 2] No such file or directory
(DAY-EC) ubuntu@ip-10-0-0-88:/fsx/analysis_results/ubuntu/ccv20260529r11_illumina_run_qc/daylily-omics-analysis$
