DAY-EC activated.
DAY-EC activated.

		# Hybrid workflow targets:

		dy-r produce_sentdhio_vcf -p -k -j 20 -n       # Hybrid Illumina+ONT CLI

		dy-r produce_sentdhuo_vcf -p -k -j 20 -n       # Hybrid Ultima+ONT CLI (use hg38_broad)

		dy-r produce_sentdhiom_vcf -p -k -j 20 -n      # Hybrid Illumina+ONT Modular

		dy-r produce_sentdhuom_vcf -p -k -j 20 -n      # Hybrid Ultima+ONT Modular (use hg38_broad)



		# Remove -n to execute (not dry-run)

Requesting profile: slurm
Attempting to deactivate existing environments & re-init with --project dyec-test .
Remote call detected. Activating conda hack
 > >> >>>
ACTIVE CONFIG FILES NOT FOUND IN /fsx/analysis_results/ubuntu/ccv20260529r45_roche_snv_alignstats_dryrun/daylily-omics-analysis/config/day_profiles/slurm ... copying
Copying template yaml files to active config files /fsx/analysis_results/ubuntu/ccv20260529r45_roche_snv_alignstats_dryrun/daylily-omics-analysis/config/day_profiles/slurm
Copying template bash files to active config files /fsx/analysis_results/ubuntu/ccv20260529r45_roche_snv_alignstats_dryrun/daylily-omics-analysis/config/day_profiles/slurm
yq is already installed.
WARNING: sentieon lic file /fsx/references/runtime_assets/cached_envs/x.lic not found.
WARNING: SENTIEON_LICENSE was not configured with a valid file; auto assigning a detected Sentieon license: /fsx/references/runtime_assets/cached_envs/Life_Sciences_Manufacturing_Corporation_eval.lic

!!!!
!!!!
    WARNING: gittag:null not found touched in  ~/.config/daylily/null
     This might be fine if you have cloned a more recent release of daylily compared to the tagged version used to create this ephemeral cluster.
     ... however, this is not expected. If you are running an ephemeral cluster headnode for days+, this is not the intended use of daylily, a fresh build might be called for.
     This is checked by testing if ~/.config/daylily/null exists .
!!!!
 > >> >>>   genome build set to ::: hg38_broad
       _______ GREAT SUCCESS _______
[INFO] Patched goleft empty-sex/no-usable-chromosomes repair: workflow/rules/go_left.smk
[INFO] Patched mosdepth empty-output repair: workflow/rules/mosdepth.smk
Remote call detected. Activating conda hack
Your config files in /fsx/analysis_results/ubuntu/ccv20260529r45_roche_snv_alignstats_dryrun/daylily-omics-analysis/config/day_profiles/slurm are newer than the templates. clear 2 go.
...AUTO-CONFIG: dedupers=na (from target rules → env)
...AUTO-CONFIG: snv_callers=sentd (from target rules → env)
Executing: snakemake --profile=/fsx/analysis_results/ubuntu/ccv20260529r45_roche_snv_alignstats_dryrun/daylily-omics-analysis/config/day_profiles/slurm produce_alignstats produce_na_dedup_cram produce_sentD_vcf -p -j 5 -k -n
loading global: /fsx/analysis_results/ubuntu/ccv20260529r45_roche_snv_alignstats_dryrun/daylily-omics-analysis/config/global_AWSPC.yaml
loading profile rule_config: /fsx/analysis_results/ubuntu/ccv20260529r45_roche_snv_alignstats_dryrun/daylily-omics-analysis/config/day_profiles/slurm/rule_config.yaml
INFO::: The genome build hg38_broad is supported.  The genome build prefix is 'chr''.
...WARNING: No aligners set in the config.
aligners (final): []
...INFO: No dedupers set in config. Defaulting to na (no dedup).
...INFO: Auto-detected dedupers. DDUP updated to: ['na']
deduper (final): [na]
...WARNING: No snv_callers set in the config.
...INFO: Auto-detected SNV callers from env: ['sentd']
SNV Callers (final): [sentd]
Somatic SNV Callers:[senttn]
... WARNING: No sv_callers set in the config.
SV Callers (final): []
A    N   A   L  Y S I S    SAMPLE TABLE DETECTED ::: /fsx/analysis_results/ubuntu/ccv20260529r45_roche_snv_alignstats_dryrun/daylily-omics-analysis/config/samples.tsv
A    N   A   L  Y S I S    UNIT TABLE DETECTED ::: /fsx/analysis_results/ubuntu/ccv20260529r45_roche_snv_alignstats_dryrun/daylily-omics-analysis/config/units.tsv
Building DAG of jobs...
PREP ROCHE BAM:: results/day/hg38_broad//TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/ ...
Job stats:
job                      count    min threads    max threads
---------------------  -------  -------------  -------------
alignstats_bam               1             96             96
alignstats_compile           1              2              2
alignstats_gather            1              1              1
finish_align_stats           1              2              2
no_dedup_roche_bam           1              1              1
pre_prep_roche_bam           1             32             32
produce_alignstats           1              1              1
produce_na_dedup_cram        1              1              1
produce_sentD_vcf            1              1              1
total                        9              1             96


[Sat May 30 12:17:49 2026]
localrule produce_sentD_vcf:
    output: gatheredall.sentd
    log: gatheredall.sentd.log
    jobid: 0
    reason: Missing output files: gatheredall.sentd
    priority: 48
    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=

( touch gatheredall.sentd ;

        ls gatheredall.sentd ) >> gatheredall.sentd.log 2>&1;


[Sat May 30 12:17:49 2026]
rule pre_prep_roche_bam:
    input: /fsx/references/genomic_data/organism_reads_slim/bam/H_sapiens/giab/roche/091025_webinar_data_giab_bam_bwa/HG003.bam
    output: results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.bam, results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.bam.bai
    log: results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/logs/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.bam.log
    jobid: 3
    benchmark: results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/benchmarks/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.downsample.bench.tsv
    reason: Missing output files: results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.bam.bai, results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.bam
    wildcards: sample=TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX, sample_lane=TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX
    threads: 32
    resources: mem_mb=64000, mem_mib=61036, disk_mb=1000, disk_mib=954, tmpdir=<TBD>, threads=32, time=5440, partition=i192mem,i192bigmem, vcpu=32, distribution=block, exclusive=, constraint=, exclude=, include=


        (mkdir -p $(dirname results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/logs/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.bam.log) || echo results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/logs/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.bam.log dir exists) >> results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/logs/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.bam.log 2>&1;

        if [[ '0.086' != 'na' ]]; then
            echo 'Downsampling Roche BAM to ratio 0.086' >> results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/logs/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.bam.log 2>&1;
            samtools view                 -@ 32                 -s 0.086                 --subsample-seed 1234                 -b                 --write-index                 -o results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.bam##idx##results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.bam.bai                 /fsx/references/genomic_data/organism_reads_slim/bam/H_sapiens/giab/roche/091025_webinar_data_giab_bam_bwa/HG003.bam >> results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/logs/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.bam.log 2>&1;
        else
            echo 'No downsampling: symlinking Roche BAM' >> results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/logs/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.bam.log 2>&1;
            ln -sf /fsx/references/genomic_data/organism_reads_slim/bam/H_sapiens/giab/roche/091025_webinar_data_giab_bam_bwa/HG003.bam results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.bam >> results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/logs/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.bam.log 2>&1;
            sleep 2;
            if [[ -f "/fsx/references/genomic_data/organism_reads_slim/bam/H_sapiens/giab/roche/091025_webinar_data_giab_bam_bwa/HG003.bam.bai" ]]; then
                ln -sf /fsx/references/genomic_data/organism_reads_slim/bam/H_sapiens/giab/roche/091025_webinar_data_giab_bam_bwa/HG003.bam.bai results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.bam.bai >> results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/logs/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.bam.log 2>&1;
            else
                samtools index -@ 32 results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.bam >> results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/logs/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.bam.log 2>&1;
            fi
        fi


[Sat May 30 12:17:49 2026]
rule no_dedup_roche_bam:
    input: results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.bam, results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.bam.bai
    output: results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/na/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.na.bam, results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/na/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.na.bam.bai
    log: results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/na/logs/no_dedup_roche.TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.log
    jobid: 2
    benchmark: results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/benchmarks/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.na.no_dedup_roche.bench.tsv
    reason: Missing output files: results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/na/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.na.bam, results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/na/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.na.bam.bai; Input files updated by another job: results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.bam.bai, results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.bam
    wildcards: sample=TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX, alnr=roche
    priority: 3
    resources: mem_mb=1000, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=<TBD>, threads=1, time=5440, partition=i192, vcpu=1, distribution=block, exclusive=, constraint=, exclude=, include=


        set -euo pipefail
        mkdir -p $(dirname results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/na/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.na.bam)
        touch results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/na/logs/no_dedup_roche.TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.log

        ln -sfn "$(realpath --relative-to=$(dirname results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/na/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.na.bam) results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.bam)" results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/na/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.na.bam >> results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/na/logs/no_dedup_roche.TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.log 2>&1
        ln -sfn "$(realpath --relative-to=$(dirname results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/na/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.na.bam.bai) results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.bam.bai)" results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/na/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.na.bam.bai >> results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/na/logs/no_dedup_roche.TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.log 2>&1

        echo "Symlinked results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.bam → results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/na/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.na.bam" >> results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/na/logs/no_dedup_roche.TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.log 2>&1
        echo "Symlinked results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.bam.bai → results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/na/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.na.bam.bai" >> results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/na/logs/no_dedup_roche.TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.log 2>&1


[Sat May 30 12:17:49 2026]
localrule produce_na_dedup_cram:
    input: results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/na/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.na.bam, results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/na/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.na.bam.bai
    output: results/day/hg38_broad/logs/target_aliases/produce_na_dedup_cram.done
    jobid: 1
    reason: Missing output files: results/day/hg38_broad/logs/target_aliases/produce_na_dedup_cram.done; Input files updated by another job: results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/na/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.na.bam, results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/na/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.na.bam.bai
    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=

mkdir -p $(dirname results/day/hg38_broad/logs/target_aliases/produce_na_dedup_cram.done); touch results/day/hg38_broad/logs/target_aliases/produce_na_dedup_cram.done;

[Sat May 30 12:17:49 2026]
rule alignstats_bam:
    input: results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/na/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.na.bam, results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/na/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.na.bam.bai
    output: results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/na/alignqc/alignstats/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.na.alignstats.json
    log: results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/na/alignqc/alignstats/logs/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.na.alignstats.log
    jobid: 8
    benchmark: results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/benchmarks/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.na.alignstats_bam.bench.tsv
    reason: Missing output files: results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/na/alignqc/alignstats/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.na.alignstats.json; Input files updated by another job: results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/na/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.na.bam, results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/na/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.na.bam.bai
    wildcards: sample=TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX, alnr=roche, ddup=na
    threads: 96
    resources: mem_mb=3000, mem_mib=2862, disk_mb=1000, disk_mib=954, tmpdir=<TBD>, threads=96, time=5440, partition=i192,i192mem,i128, vcpu=96, distribution=block, exclusive=, constraint=, exclude=, include=, attempt_n=1

resources/alignstats/alignstats  -C -U  -i results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/na/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.na.bam -T /fsx/references/genomic_data/organism_references/H_sapiens/hg38_broad/Homo_sapiens_assembly38.fasta -o results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/na/alignqc/alignstats/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.na.alignstats.json  -j bam -v -P 96 -p 96 > results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/na/alignqc/alignstats/logs/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.na.alignstats.log;

[Sat May 30 12:17:49 2026]
localrule finish_align_stats:
    input: results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/na/alignqc/alignstats/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.na.alignstats.json
    output: results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/na/alignqc/alignstats/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.na.alignstats.tsv
    jobid: 7
    reason: Missing output files: results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/na/alignqc/alignstats/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.na.alignstats.tsv; Input files updated by another job: results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/na/alignqc/alignstats/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.na.alignstats.json
    wildcards: sample=TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX, alnr=roche, ddup=na
    threads: 2
    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 12:17:49 2026]
localrule alignstats_gather:
    input: results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/na/alignqc/alignstats/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.na.alignstats.tsv
    output: results/day/hg38_broad/other_reports/alignstats_summary_gather.done, results/day/hg38_broad/benchmarks/all.alignstats_summary.bench.tsv
    log: results/day/hg38_broad/logs/alignstats_summary_gather.log
    jobid: 6
    benchmark: results/day/hg38_broad/benchmarks/all.alignstats_summary.bench.tsv
    reason: Missing output files: results/day/hg38_broad/other_reports/alignstats_summary_gather.done; Input files updated by another job: results/day/hg38_broad/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX/align/roche/na/alignqc/alignstats/TVBROCHE5X-HG003-5x-0-D0-PF-ROCHE-SBX-DUPLEX.roche.na.alignstats.tsv
    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=

 touch results/day/hg38_broad/other_reports/alignstats_summary_gather.done; touch results/day/hg38_broad/benchmarks/all.alignstats_summary.bench.tsv

[Sat May 30 12:17:49 2026]
localrule alignstats_compile:
    input: results/day/hg38_broad/other_reports/alignstats_summary_gather.done
    output: results/day/hg38_broad/other_reports/alignstats_bsummary.tsv, results/day/hg38_broad/other_reports/alignstats_csummary.tsv, results/day/hg38_broad/other_reports/alignstats_combo_mqc.tsv, results/day/hg38_broad/other_reports/alignstats_gs_mqc.tsv
    log: results/day/hg38_broad/logs/alignstats_summary_compile.log
    jobid: 5
    benchmark: results/day/hg38_broad/benchmarks/all.alignstats_smmary_compile.bench.tsv
    reason: Missing output files: results/day/hg38_broad/other_reports/alignstats_bsummary.tsv; Input files updated by another job: results/day/hg38_broad/other_reports/alignstats_summary_gather.done
    threads: 2
    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
        python workflow/scripts/compile_alignstats.py           --mdir results/day/hg38_broad/           --log results/day/hg38_broad/logs/alignstats_summary_compile.log           --bsummary results/day/hg38_broad/other_reports/alignstats_bsummary.tsv           --csummary results/day/hg38_broad/other_reports/alignstats_csummary.tsv           --combo results/day/hg38_broad/other_reports/alignstats_combo_mqc.tsv           --generalstats results/day/hg38_broad/other_reports/alignstats_gs_mqc.tsv

Would remove temporary output results/day/hg38_broad/other_reports/alignstats_csummary.tsv

[Sat May 30 12:17:49 2026]
localrule produce_alignstats:
    input: results/day/hg38_broad/other_reports/alignstats_bsummary.tsv
    jobid: 4
    reason: Input files updated by another job: results/day/hg38_broad/other_reports/alignstats_bsummary.tsv
    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=

Would remove temporary output results/day/hg38_broad/other_reports/alignstats_bsummary.tsv
Job stats:
job                      count    min threads    max threads
---------------------  -------  -------------  -------------
alignstats_bam               1             96             96
alignstats_compile           1              2              2
alignstats_gather            1              1              1
finish_align_stats           1              2              2
no_dedup_roche_bam           1              1              1
pre_prep_roche_bam           1             32             32
produce_alignstats           1              1              1
produce_na_dedup_cram        1              1              1
produce_sentD_vcf            1              1              1
total                        9              1             96

Reasons:
    (check individual jobs above for details)
    input files updated by another job:
        alignstats_bam, alignstats_compile, alignstats_gather, finish_align_stats, no_dedup_roche_bam, produce_alignstats, produce_na_dedup_c--output truncated--
