DAY-EC activated.
DAY-EC activated.
files
-rw-rw-r-- 1 ubuntu ubuntu 13M Jun  6 10:06 results/day/hg38/reports/DAY_final_multiqc.html
-rw-rw-r-- 1 ubuntu ubuntu 26M Jun  6 10:06 results/day/hg38/reports/DAY_final_multiqc_data/multiqc_data.json
MISSING results/day/hg38/reports/dayoa_evidence_manifest.json
-rw-rw-r-- 1 ubuntu ubuntu 9.9K Jun  6 10:06 results/day/hg38/reports/logs/all__mqc_fin_a.log
MISSING results/day/hg38/logs/produce_multiqc_all.log
slurm_job_891
     JOBID ST         TIME     CPUS    PARTITION                                                         NAME
controllers
ubuntu    498261   53952  0 10:01 ?        00:00:00 sh -c cat >> /home/ubuntu/daylily-runs/hybonly_ilmn_final_multiqc_file_20260606T100052Z/tmux.log
ubuntu    498749  498258  0 10:01 pts/12   00:00:00 bash bin/day_run produce_multiqc_all results/day/hg38/reports/DAY_final_multiqc.html results/day/hg38/reports/dayoa_evidence_manifest.json --config aligners=["sent"] dedupers=["dmd"] snv_callers=["sentd"] htd_callers=["cyrius"] multiqc_qc={"enable_tools":["vep","metagenomics","contam_identity"]} -j 200 -p -k --rerun-triggers mtime
ubuntu    498965  498749  0 10:01 pts/12   00:00:00 bash bin/day_run produce_multiqc_all results/day/hg38/reports/DAY_final_multiqc.html results/day/hg38/reports/dayoa_evidence_manifest.json --config aligners=["sent"] dedupers=["dmd"] snv_callers=["sentd"] htd_callers=["cyrius"] multiqc_qc={"enable_tools":["vep","metagenomics","contam_identity"]} -j 200 -p -k --rerun-triggers mtime
ubuntu    498966  498965  1 10:01 pts/12   00:00:06 /home/ubuntu/miniconda3/envs/DAYOA/bin/python /home/ubuntu/miniconda3/envs/DAYOA/bin/snakemake --profile=/fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/config/day_profiles/slurm produce_multiqc_all results/day/hg38/reports/DAY_final_multiqc.html results/day/hg38/reports/dayoa_evidence_manifest.json --config aligners=["sent"] dedupers=["dmd"] snv_callers=["sentd"] htd_callers=["cyrius"] multiqc_qc={"enable_tools":["vep","metagenomics","contam_identity"]} -j 200 -p -k --rerun-triggers mtime
ubuntu    498967  498965  0 10:01 pts/12   00:00:00 bash bin/day_run produce_multiqc_all results/day/hg38/reports/DAY_final_multiqc.html results/day/hg38/reports/dayoa_evidence_manifest.json --config aligners=["sent"] dedupers=["dmd"] snv_callers=["sentd"] htd_callers=["cyrius"] multiqc_qc={"enable_tools":["vep","metagenomics","contam_identity"]} -j 200 -p -k --rerun-triggers mtime
ubuntu    502270  498966  0 10:06 pts/12   00:00:00 /bin/sh -c cd /fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis && /home/ubuntu/miniconda3/envs/DAYOA/bin/python -m snakemake --snakefile '/fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/workflow/Snakefile' --target-jobs 'write_dayoa_evidence_manifest:' --allowed-rules 'write_dayoa_evidence_manifest' --cores 8 --attempt 1 --force-use-threads  --resources 'mem_mb=3000' 'mem_mib=2862' 'disk_mb=1000' 'disk_mib=954' 'threads=1' 'time=5440' 'vcpu=1' --quiet --force --keep-target-files --keep-remote --max-inventory-time 0 --nocolor --notemp --no-hooks --nolock --ignore-incomplete --rerun-triggers 'mtime' --skip-script-cleanup  --use-conda  --conda-frontend 'conda' --conda-prefix '/fsx/resources/environments/conda/ubuntu/ip-10-0-0-81' --conda-base-path '/home/ubuntu/miniconda3' --use-singularity  --singularity-prefix '/fsx/resources/environments/containers/ubuntu/ip-10-0-0-81' --singularity-args '  -B /fsx:/fsx -B /tmp:/tmp -B $PWD/:$PWD   -B /dev/fd:/dev/fd  -B /dev/shm:$PWD/resources/dev/shm -B /dev/shm:/dev/shm ' --wrapper-prefix 'https://github.com/snakemake/snakemake-wrappers/raw/' --local-groupid 'local' --config 'aligners=["sent"]' 'dedupers=["dmd"]' 'snv_callers=["sentd"]' 'htd_callers=["cyrius"]' 'multiqc_qc={"enable_tools":["vep","metagenomics","contam_identity"]}' --printshellcmds  --latency-wait 100 --scheduler 'greedy' --scheduler-solver-path '/home/ubuntu/miniconda3/envs/DAYOA/bin' --default-resources 'mem_mb=3000' 'disk_mb=1000' 'tmpdir=system_tmpdir' 'threads=1' 'time=5440' 'partition=i192,i128,i192mem,bcl2fq-i384-nvme-test' 'vcpu=1' 'distribution=block' "exclusive=''" "constraint=''" "exclude=''" "include=''" --mode 1
ubuntu    502271  502270 85 10:06 pts/12   00:00:49 /home/ubuntu/miniconda3/envs/DAYOA/bin/python -m snakemake --snakefile /fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/workflow/Snakefile --target-jobs write_dayoa_evidence_manifest: --allowed-rules write_dayoa_evidence_manifest --cores 8 --attempt 1 --force-use-threads --resources mem_mb=3000 mem_mib=2862 disk_mb=1000 disk_mib=954 threads=1 time=5440 vcpu=1 --quiet --force --keep-target-files --keep-remote --max-inventory-time 0 --nocolor --notemp --no-hooks --nolock --ignore-incomplete --rerun-triggers mtime --skip-script-cleanup --use-conda --conda-frontend conda --conda-prefix /fsx/resources/environments/conda/ubuntu/ip-10-0-0-81 --conda-base-path /home/ubuntu/miniconda3 --use-singularity --singularity-prefix /fsx/resources/environments/containers/ubuntu/ip-10-0-0-81 --singularity-args   -B /fsx:/fsx -B /tmp:/tmp -B $PWD/:$PWD   -B /dev/fd:/dev/fd  -B /dev/shm:$PWD/resources/dev/shm -B /dev/shm:/dev/shm  --wrapper-prefix https://github.com/snakemake/snakemake-wrappers/raw/ --local-groupid local --config aligners=["sent"] dedupers=["dmd"] snv_callers=["sentd"] htd_callers=["cyrius"] multiqc_qc={"enable_tools":["vep","metagenomics","contam_identity"]} --printshellcmds --latency-wait 100 --scheduler greedy --scheduler-solver-path /home/ubuntu/miniconda3/envs/DAYOA/bin --default-resources mem_mb=3000 disk_mb=1000 tmpdir=system_tmpdir threads=1 time=5440 partition=i192,i128,i192mem,bcl2fq-i384-nvme-test vcpu=1 distribution=block exclusive='' constraint='' exclude='' include='' --mode 1
tmux_tail
    reason: Missing output files: results/day/hg38/reports/DAY_final_multiqc_data/multiqc_general_stats.txt, results/day/hg38/reports/DAY_final_multiqc_data/multiqc_data.json, results/day/hg38/reports/DAY_final_multiqc_data/multiqc.log, results/day/hg38/reports/DAY_final_multiqc_data/multiqc_sources.txt, results/day/hg38/reports/DAY_final_multiqc.html; Input files updated by another job: results/day/hg38/other_reports/rules_benchmark_data_mqc.tsv, results/day/hg38/logs/report_components_aggregated.done, results/day/hg38/reports/multiqc_inputs/final/.stage.done, results/day/hg38/reports/multiqc_inputs/final/manifest.tsv
    priority: 50
    threads: 4
    resources: mem_mb=3000, mem_mib=2862, disk_mb=1000, disk_mib=954, tmpdir=<TBD>, threads=4, time=5440, partition=i192,i192mem,i128, vcpu=1, distribution=block, exclusive=, constraint=, exclude=, include=[0m
[32m[0m
[33m
        dbill='$';
        mkdir -p $(dirname results/day/hg38/reports/DAY_final_multiqc.html) $(dirname results/day/hg38/reports/logs/all__mqc_fin_a.log)
        python workflow/scripts/multiqc_log_guard.py --log-dir results/day/hg38/other_reports/logs > results/day/hg38/reports/logs/all__mqc_fin_a.log 2>&1
        multiqc --version >> results/day/hg38/reports/logs/all__mqc_fin_a.log 2>&1 || true
        echo '''
report_header_info:
  - Project/Budget: "REGSUB_PROJECT"
  - Budget @ Runtime: "REGSUB_BUDGET"
  - Spot Instances: "REGSUB_SPOTINSTANCES"
  - Spot Costs per hr: "REGSUB_SPOTCOST"
  - FQ->BAM.sort avg Costs: "REGSUB_TOTALCOST"
  - BAM mrkdup avg Cost: "REGSUB_MRKDUPCOST"
  - Results Dir (GB): "REGSUB_TOTALSIZE"
  ''' > results/day/hg38/reports/multiqc_header.yaml 2>> results/day/hg38/reports/logs/all__mqc_fin_a.log;

        perl -pi -e "s/REGSUB_PROJECT/$DAY_PROJECT/g;"  results/day/hg38/reports/multiqc_header.yaml >> results/day/hg38/reports/logs/all__mqc_fin_a.log 2>&1;
        perl -pi -e "s/REGSUB_BUDGET/\\$dbill$USED_BUDGET of \\$dbill$TOTAL_BUDGET spent ( $PERCENT_USED\%)/g;" results/day/hg38/reports/multiqc_header.yaml >> results/day/hg38/reports/logs/all__mqc_fin_a.log 2>&1;

        size=$(du -hs results | cut -f1) >> results/day/hg38/reports/logs/all__mqc_fin_a.log 2>&1;
        perl -pi -e "s/REGSUB_TOTALSIZE/$size/g;" results/day/hg38/reports/multiqc_header.yaml >> results/day/hg38/reports/logs/all__mqc_fin_a.log 2>&1;

        source bin/proc_spot_price_logs.sh >> results/day/hg38/reports/logs/all__mqc_fin_a.log 2>&1;
        perl -pi -e "s/REGSUB_SPOTCOST/median: \\$dbill$MEDIAN_SPOT_PRICE  mean: \\$dbill$AVERAGE_SPOT_PRICE ( avg cost per vcpu,per min: \\$dbill$VCPU_COST_PER_MIN ) /g;"  results/day/hg38/reports/multiqc_header.yaml >> results/day/hg38/reports/logs/all__mqc_fin_a.log 2>&1;
        perl -pi -e "s/REGSUB_SPOTINSTANCES/ $INSTANCE_TYPES_LINE /g;" results/day/hg38/reports/multiqc_header.yaml >> results/day/hg38/reports/logs/all__mqc_fin_a.log 2>&1;

        source bin/proc_aligner_costs.sh results/day/hg38/other_reports/rules_benchmark_data_mqc.tsv $VCPU_COST_PER_MIN >> results/day/hg38/reports/logs/all__mqc_fin_a.log 2>&1;
        perl -pi -e "s/REGSUB_TOTALCOST/$ALNR_SUMMARY_COST/g;" results/day/hg38/reports/multiqc_header.yaml >> results/day/hg38/reports/logs/all__mqc_fin_a.log 2>&1;

        source bin/proc_mrkdup_costs.sh results/day/hg38/other_reports/rules_benchmark_data_mqc.tsv $VCPU_COST_PER_MIN  >> results/day/hg38/reports/logs/all__mqc_fin_a.log 2>&1;
        perl -pi -e "s/REGSUB_MRKDUPCOST/$MRKDUP_AVG_MINUTES min, costing \\$dbill$MRKDUP_AVG_COST/g;" results/day/hg38/reports/multiqc_header.yaml >> results/day/hg38/reports/logs/all__mqc_fin_a.log 2>&1;

        module_excludes="$(python workflow/scripts/multiqc_module_exclude_args.py config/multiqc_module_exclude.txt)"
        multiqc -f          $module_excludes         --config results/day/hg38/reports/multiqc_header.yaml         --config ./config/external_tools/multiqc_config.yaml          --custom-css-file ./config/external_tools/multiqc.css         --ignore "*/other_reports/logs/*"         --ignore "other_reports/logs/*"         --ignore "*_mqc.log"         --template default         --filename results/day/hg38/reports/DAY_final_multiqc.html         -i 'Final Multiqc Report '         -b 'https://github.com/lsmc-bio/daylily-omics-analysis (BRANCH:* jem-dev) (TAG:5.0.2) (HASH:d02a1bd) '         results/day/hg38/reports/multiqc_inputs/final >> results/day/hg38/reports/logs/all__mqc_fin_a.log 2>&1;
        python workflow/scripts/force_multiqc_dark_mode.py           --html results/day/hg38/reports/DAY_final_multiqc.html           --backup results/day/hg38/reports/DAY_final_multiqc.original.html >> results/day/hg38/reports/logs/all__mqc_fin_a.log 2>&1;
        python workflow/scripts/validate_multiqc_sample_ids.py           --manifest results/day/hg38/reports/multiqc_inputs/final/manifest.tsv           --multiqc-data results/day/hg38/reports/DAY_final_multiqc_data/multiqc_data.json >> results/day/hg38/reports/logs/all__mqc_fin_a.log 2>&1;
        ls -lt results/day/hg38/reports/DAY_final_multiqc.html results/day/hg38/reports/DAY_final_multiqc.original.html results/day/hg38/reports/multiqc_header.yaml >> results/day/hg38/reports/logs/all__mqc_fin_a.log 2>&1;
        [0m
[33mSubmitted job 1 with external jobid '891'.[0m
[32m[Sat Jun  6 10:06:54 2026][0m
[32mFinished job 1.[0m
[32m5 of 7 steps (71%) done[0m
[33mSelect jobs to execute...[0m
[32m[0m
[32m[Sat Jun  6 10:06:54 2026][0m
[32mlocalrule write_dayoa_evidence_manifest:
    input: results/day/hg38/reports/DAY_final_multiqc.html, results/day/hg38/reports/DAY_final_multiqc_data/multiqc_data.json, results/day/hg38/reports/DAY_final_multiqc_data/multiqc_general_stats.txt, results/day/hg38/reports/DAY_final_multiqc_data/multiqc_sources.txt, results/day/hg38/reports/DAY_final_multiqc_data/multiqc.log, results/day/hg38/reports/multiqc_inputs/final/manifest.tsv, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-HG003-a-GIAB-all-S7-PF-ILMN-NOVASEQ/seqqc/fastqc/20260526-LH01121-0004-B23WW2NLT4-HG003-a-GIAB-all-S7-PF-ILMN-NOVASEQ.fastqc.done, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ/seqqc/fastqc/20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ.fastqc.done, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-HG003-c-GIAB-all-S9-PF-ILMN-NOVASEQ/seqqc/fastqc/20260526-LH01121-0004-B23WW2NLT4-HG003-c-GIAB-all-S9-PF-ILMN-NOVASEQ.fastqc.done, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA00232-SMN-all-S46-PF-ILMN-NOVASEQ/seqqc/fastqc/20260526-LH01121-0004-B23WW2NLT4-NA00232-SMN-all-S46-PF-ILMN-NOVASEQ.fastqc.done, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ/seqqc/fastqc/20260526-LH01121-0004-B23WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ.fastqc.done, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA05164-DMPK-all-S49-PF-ILMN-NOVASEQ/seqqc/fastqc/20260526-LH01121-0004-B23WW2NLT4-NA05164-DMPK-all-S49-PF-ILMN-NOVASEQ.fastqc.done, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA09677-SMN-all-S47-PF-ILMN-NOVASEQ/seqqc/fastqc/20260526-LH01121-0004-B23WW2NLT4-NA09677-SMN-all-S47-PF-ILMN-NOVASEQ.fastqc.done, results/day/hg38/other_reports/seqfu_mqc.tsv, results/day/hg38/other_reports/input_sample_libraries_mqc.tsv, results/day/hg38/other_reports/sequence_qc_outputs_mqc.tsv, results/day/hg38/other_reports/alignstats_combo_mqc.tsv, results/day/hg38/other_reports/norm_cov_evenness_combo_mqc.tsv, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-HG003-a-GIAB-all-S7-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/samtmetrics/20260526-LH01121-0004-B23WW2NLT4-HG003-a-GIAB-all-S7-PF-ILMN-NOVASEQ.sent.dmd.complete, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-HG003-a-GIAB-all-S7-PF-ILMN-NOVASEQ/align/sent/na/alignqc/samtmetrics/20260526-LH01121-0004-B23WW2NLT4-HG003-a-GIAB-all-S7-PF-ILMN-NOVASEQ.sent.na.complete, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/samtmetrics/20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ.sent.dmd.complete, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ/align/sent/na/alignqc/samtmetrics/20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ.sent.na.complete, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-HG003-c-GIAB-all-S9-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/samtmetrics/20260526-LH01121-0004-B23WW2NLT4-HG003-c-GIAB-all-S9-PF-ILMN-NOVASEQ.sent.dmd.complete, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-HG003-c-GIAB-all-S9-PF-ILMN-NOVASEQ/align/sent/na/alignqc/samtmetrics/20260526-LH01121-0004-B23WW2NLT4-HG003-c-GIAB-all-S9-PF-ILMN-NOVASEQ.sent.na.complete, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA00232-SMN-all-S46-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/samtmetrics/20260526-LH01121-0004-B23WW2NLT4-NA00232-SMN-all-S46-PF-ILMN-NOVASEQ.sent.dmd.complete, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA00232-SMN-all-S46-PF-ILMN-NOVASEQ/align/sent/na/alignqc/samtmetrics/20260526-LH01121-0004-B23WW2NLT4-NA00232-SMN-all-S46-PF-ILMN-NOVASEQ.sent.na.complete, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/samtmetrics/20260526-LH01121-0004-B23WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ.sent.dmd.complete, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ/align/sent/na/alignqc/samtmetrics/20260526-LH01121-0004-B23WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ.sent.na.complete, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA05164-DMPK-all-S49-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/samtmetrics/20260526-LH01121-0004-B23WW2NLT4-NA05164-DMPK-all-S49-PF-ILMN-NOVASEQ.sent.dmd.complete, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA05164-DMPK-all-S49-PF-ILMN-NOVASEQ/align/sent/na/alignqc/samtmetrics/20260526-LH01121-0004-B23WW2NLT4-NA05164-DMPK-all-S49-PF-ILMN-NOVASEQ.sent.na.complete, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA09677-SMN-all-S47-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/samtmetrics/20260526-LH01121-0004-B23WW2NLT4-NA09677-SMN-all-S47-PF-ILMN-NOVASEQ.sent.dmd.complete, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA09677-SMN-all-S47-PF-ILMN-NOVASEQ/align/sent/na/alignqc/samtmetrics/20260526-LH01121-0004-B23WW2NLT4-NA09677-SMN-all-S47-PF-ILMN-NOVASEQ.sent.na.complete, results/day/hg38/other_reports/samtools_metrics_gather.done, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-HG003-a-GIAB-all-S7-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/mosdepth/20260526-LH01121-0004-B23WW2NLT4-HG003-a-GIAB-all-S7-PF-ILMN-NOVASEQ.sent.dmd.mosdepth.summary.txt, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-HG003-a-GIAB-all-S7-PF-ILMN-NOVASEQ/align/sent/na/alignqc/mosdepth/20260526-LH01121-0004-B23WW2NLT4-HG003-a-GIAB-all-S7-PF-ILMN-NOVASEQ.sent.na.mosdepth.summary.txt, 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