DAY-EC activated.
DAY-EC activated.
[Errno 2] No such file or directory: '/fsx/control_data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/downsampled/HG003_40x_R1.fastq.gz'
[Errno 2] No such file or directory: '/fsx/control_data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/downsampled/HG003_1x_R1.fastq.gz'
[Errno 2] No such file or directory: '/fsx/control_data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/downsampled/HG003_3x_R1.fastq.gz'
[Errno 2] No such file or directory: '/fsx/control_data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/downsampled/HG003_5x_R1.fastq.gz'
[Errno 2] No such file or directory: '/fsx/control_data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/downsampled/HG003_7x_R1.fastq.gz'
[Errno 2] No such file or directory: '/fsx/control_data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/downsampled/HG003_10x_R1.fastq.gz'
[Errno 2] No such file or directory: '/fsx/control_data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/downsampled/HG003_15x_R1.fastq.gz'
[Errno 2] No such file or directory: '/fsx/control_data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/downsampled/HG003_20x_R1.fastq.gz'
[Errno 2] No such file or directory: '/fsx/control_data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG003_30x_R1.fastq.gz'
[Errno 2] No such file or directory: '/fsx/control_data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/downsampled/HG003_40x_R1.fastq.gz'
Building DAG of jobs...
Using shell: /home/ubuntu/miniconda3/envs/DAY-EC/bin/bash
Provided cluster nodes: 5
Job stats:
job                             count    min threads    max threads
----------------------------  -------  -------------  -------------
ont_run_qc_collect_summaries        1              1              1
ont_run_qc_multiqc                  1              1              1
ont_run_qc_nanoplot                 1              8              8
ont_run_qc_pycoqc                   1              1              1
ont_run_qc_report                   1              1              1
produce_ont_run_qc                  1              1              1
total                               6              1              8

Select jobs to execute...

[Sat May 30 06:00:04 2026]
localrule ont_run_qc_collect_summaries:
    output: results/runs/20260513_ONT_HG003/run_qc/ont/tables/sequencing_summary_files.txt
    log: results/runs/20260513_ONT_HG003/run_qc/ont/logs/collect_summaries.log
    jobid: 3
    benchmark: results/runs/20260513_ONT_HG003/run_qc/ont/benchmarks/collect_summaries.bench.tsv
    reason: Missing output files: results/runs/20260513_ONT_HG003/run_qc/ont/tables/sequencing_summary_files.txt
    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/20260513_ONT_HG003/run_qc/ont/tables/sequencing_summary_files.txt) $(dirname results/runs/20260513_ONT_HG003/run_qc/ont/logs/collect_summaries.log)
        : > results/runs/20260513_ONT_HG003/run_qc/ont/logs/collect_summaries.log
        if [ -z /fsx/run_dir_mounts/20260513_ONT_HG003/ ]; then
            echo "config/runs.tsv with PLATFORM=ONT and RUN_DIR is required for mounted ONT run QC" >> results/runs/20260513_ONT_HG003/run_qc/ont/logs/collect_summaries.log
            exit 2
        fi
        test -d /fsx/run_dir_mounts/20260513_ONT_HG003/
        find /fsx/run_dir_mounts/20260513_ONT_HG003/ -type f \( -name 'sequencing_summary*.txt' -o -name 'sequencing_summary*.txt.gz' \) \
          | sort > results/runs/20260513_ONT_HG003/run_qc/ont/tables/sequencing_summary_files.txt
        if [ ! -s results/runs/20260513_ONT_HG003/run_qc/ont/tables/sequencing_summary_files.txt ]; then
            echo "No sequencing_summary*.txt files found under /fsx/run_dir_mounts/20260513_ONT_HG003/" >> results/runs/20260513_ONT_HG003/run_qc/ont/logs/collect_summaries.log
            exit 2
        fi
        
Activating conda environment: ../../../../resources/environments/conda/ubuntu/ip-10-0-0-88/a99ea18d415639f67a6e85afdbe2fe1b_
[Sat May 30 06:00:04 2026]
Finished job 3.
1 of 6 steps (17%) done
Select jobs to execute...

[Sat May 30 06:00:04 2026]
localrule ont_run_qc_pycoqc:
    input: results/runs/20260513_ONT_HG003/run_qc/ont/tables/sequencing_summary_files.txt
    output: results/runs/20260513_ONT_HG003/run_qc/ont/pycoqc/pycoQC.html, results/runs/20260513_ONT_HG003/run_qc/ont/pycoqc/pycoQC.json
    log: results/runs/20260513_ONT_HG003/run_qc/ont/logs/pycoqc.log
    jobid: 2
    benchmark: results/runs/20260513_ONT_HG003/run_qc/ont/benchmarks/pycoqc.bench.tsv
    reason: Missing output files: results/runs/20260513_ONT_HG003/run_qc/ont/pycoqc/pycoQC.json, results/runs/20260513_ONT_HG003/run_qc/ont/pycoqc/pycoQC.html; Input files updated by another job: results/runs/20260513_ONT_HG003/run_qc/ont/tables/sequencing_summary_files.txt
    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 results/runs/20260513_ONT_HG003/run_qc/ont/pycoqc $(dirname results/runs/20260513_ONT_HG003/run_qc/ont/logs/pycoqc.log)
        : > results/runs/20260513_ONT_HG003/run_qc/ont/logs/pycoqc.log
        command -v pycoQC >> results/runs/20260513_ONT_HG003/run_qc/ont/logs/pycoqc.log 2>&1
        mapfile -t summary_files < results/runs/20260513_ONT_HG003/run_qc/ont/tables/sequencing_summary_files.txt
        pycoQC \
          -f "${summary_files[@]}" \
          -o results/runs/20260513_ONT_HG003/run_qc/ont/pycoqc/pycoQC.html \
          -j results/runs/20260513_ONT_HG003/run_qc/ont/pycoqc/pycoQC.json \
          --report_title 20260513_ONT_HG003 \
          >> results/runs/20260513_ONT_HG003/run_qc/ont/logs/pycoqc.log 2>&1
        test -s results/runs/20260513_ONT_HG003/run_qc/ont/pycoqc/pycoQC.html
        test -s results/runs/20260513_ONT_HG003/run_qc/ont/pycoqc/pycoQC.json
        
Activating conda environment: ../../../../resources/environments/conda/ubuntu/ip-10-0-0-88/a99ea18d415639f67a6e85afdbe2fe1b_

[Sat May 30 06:00:04 2026]
localrule ont_run_qc_nanoplot:
    input: results/runs/20260513_ONT_HG003/run_qc/ont/tables/sequencing_summary_files.txt
    output: results/runs/20260513_ONT_HG003/run_qc/ont/nanoplot/nanoplot.done
    log: results/runs/20260513_ONT_HG003/run_qc/ont/logs/nanoplot.log
    jobid: 5
    benchmark: results/runs/20260513_ONT_HG003/run_qc/ont/benchmarks/nanoplot.bench.tsv
    reason: Missing output files: results/runs/20260513_ONT_HG003/run_qc/ont/nanoplot/nanoplot.done; Input files updated by another job: results/runs/20260513_ONT_HG003/run_qc/ont/tables/sequencing_summary_files.txt
    threads: 8
    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 results/runs/20260513_ONT_HG003/run_qc/ont/nanoplot $(dirname results/runs/20260513_ONT_HG003/run_qc/ont/logs/nanoplot.log)
        : > results/runs/20260513_ONT_HG003/run_qc/ont/logs/nanoplot.log
        command -v NanoPlot >> results/runs/20260513_ONT_HG003/run_qc/ont/logs/nanoplot.log 2>&1
        mapfile -t summary_files < results/runs/20260513_ONT_HG003/run_qc/ont/tables/sequencing_summary_files.txt
        NanoPlot \
          --summary "${summary_files[@]}" \
          --loglength \
          --tsv_stats \
          --info_in_report \
          -t 8 \
          -o results/runs/20260513_ONT_HG003/run_qc/ont/nanoplot \
          -p 20260513_ONT_HG003. \
          >> results/runs/20260513_ONT_HG003/run_qc/ont/logs/nanoplot.log 2>&1
        
Activating conda environment: ../../../../resources/environments/conda/ubuntu/ip-10-0-0-88/a99ea18d415639f67a6e85afdbe2fe1b_
Touching output file results/runs/20260513_ONT_HG003/run_qc/ont/nanoplot/nanoplot.done.
[Sat May 30 06:00:47 2026]
Finished job 5.
2 of 6 steps (33%) done
[Sat May 30 06:00:50 2026]
Finished job 2.
3 of 6 steps (50%) done
Select jobs to execute...

[Sat May 30 06:00:50 2026]
localrule ont_run_qc_multiqc:
    input: results/runs/20260513_ONT_HG003/run_qc/ont/pycoqc/pycoQC.html, results/runs/20260513_ONT_HG003/run_qc/ont/pycoqc/pycoQC.json, results/runs/20260513_ONT_HG003/run_qc/ont/nanoplot/nanoplot.done
    output: results/runs/20260513_ONT_HG003/run_qc/ont/multiqc_report.html
    log: results/runs/20260513_ONT_HG003/run_qc/ont/logs/multiqc.log
    jobid: 4
    benchmark: results/runs/20260513_ONT_HG003/run_qc/ont/benchmarks/multiqc.bench.tsv
    reason: Missing output files: results/runs/20260513_ONT_HG003/run_qc/ont/multiqc_report.html; Input files updated by another job: results/runs/20260513_ONT_HG003/run_qc/ont/nanoplot/nanoplot.done, results/runs/20260513_ONT_HG003/run_qc/ont/pycoqc/pycoQC.json, results/runs/20260513_ONT_HG003/run_qc/ont/pycoqc/pycoQC.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=


        set -euo pipefail
        mkdir -p $(dirname results/runs/20260513_ONT_HG003/run_qc/ont/multiqc_report.html) $(dirname results/runs/20260513_ONT_HG003/run_qc/ont/logs/multiqc.log)
        multiqc --version > results/runs/20260513_ONT_HG003/run_qc/ont/logs/multiqc.log 2>&1 || true
        multiqc -f \
          -m pycoqc \
          -m nanostat \
          --filename "$(basename results/runs/20260513_ONT_HG003/run_qc/ont/multiqc_report.html)" \
          --outdir "$(dirname results/runs/20260513_ONT_HG003/run_qc/ont/multiqc_report.html)" \
          results/runs/20260513_ONT_HG003/run_qc/ont >> results/runs/20260513_ONT_HG003/run_qc/ont/logs/multiqc.log 2>&1
        test -s results/runs/20260513_ONT_HG003/run_qc/ont/multiqc_report.html
        
Activating conda environment: ../../../../resources/environments/conda/ubuntu/ip-10-0-0-88/73dbbd9209dde9d5b560eca76639c2a0_

[Sat May 30 06:00:50 2026]
localrule ont_run_qc_report:
    input: results/runs/20260513_ONT_HG003/run_qc/ont/pycoqc/pycoQC.json
    output: results/runs/20260513_ONT_HG003/run_qc/ont/summary.html, results/runs/20260513_ONT_HG003/run_qc/ont/summary.tsv, results/runs/20260513_ONT_HG003/run_qc/ont/logs/ont_run_qc_report.done
    log: results/runs/20260513_ONT_HG003/run_qc/ont/logs/ont_run_qc_report.log
    jobid: 1
    benchmark: results/runs/20260513_ONT_HG003/run_qc/ont/benchmarks/ont_run_qc_report.bench.tsv
    reason: Missing output files: results/runs/20260513_ONT_HG003/run_qc/ont/logs/ont_run_qc_report.done; Input files updated by another job: results/runs/20260513_ONT_HG003/run_qc/ont/pycoqc/pycoQC.json
    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/20260513_ONT_HG003/run_qc/ont/summary.html) $(dirname results/runs/20260513_ONT_HG003/run_qc/ont/summary.tsv) $(dirname results/runs/20260513_ONT_HG003/run_qc/ont/logs/ont_run_qc_report.log)
        python workflow/scripts/summarize_run_qc_report.py \
          --platform ONT \
          --run-s3-uri s3://lsmc-ssf-sequencing-data/basecalls/lsmc/ssf-hq/pca100/2026/20260513_ONT_HG003/ \
          --metrics-path results/runs/20260513_ONT_HG003/run_qc/ont/pycoqc/pycoQC.json \
          --output-html results/runs/20260513_ONT_HG003/run_qc/ont/summary.html \
          --output-tsv results/runs/20260513_ONT_HG003/run_qc/ont/summary.tsv \
          --done results/runs/20260513_ONT_HG003/run_qc/ont/logs/ont_run_qc_report.done > results/runs/20260513_ONT_HG003/run_qc/ont/logs/ont_run_qc_report.log 2>&1
        
Activating conda environment: ../../../../resources/environments/conda/ubuntu/ip-10-0-0-88/a99ea18d415639f67a6e85afdbe2fe1b_
[Sat May 30 06:00:51 2026]
Finished job 1.
4 of 6 steps (67%) done
[Sat May 30 06:01:03 2026]
Finished job 4.
5 of 6 steps (83%) done
Select jobs to execute...

[Sat May 30 06:01:03 2026]
localrule produce_ont_run_qc:
    input: results/runs/20260513_ONT_HG003/run_qc/ont/logs/ont_run_qc_report.done, results/runs/20260513_ONT_HG003/run_qc/ont/multiqc_report.html
    jobid: 0
    reason: Input files updated by another job: results/runs/20260513_ONT_HG003/run_qc/ont/logs/ont_run_qc_report.done, results/runs/20260513_ONT_HG003/run_qc/ont/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 06:01:03 2026]
Finished job 0.
6 of 6 steps (100%) done
Complete log: .snakemake/log/2026-05-30T055959.652702.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 06:01:06,822 INFO Found credentials from IAM Role: dyec-test-RoleHeadNode-eJMKI1vZVQBE
