DAY-EC activated.
DAY-EC activated.
    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/602221-20260417-2346-S21-B-Z0317-CTGCGCAGCATCCTGAT-prod-cram-11-CTGCGCAGCATCCTGAT-PF-UG-ULTIMA/align/ug/na/602221-20260417-2346-S21-B-Z0317-CTGCGCAGCATCCTGAT-prod-cram-11-CTGCGCAGCATCCTGAT-PF-UG-ULTIMA.ug.na.cram)
        touch results/day/hg38_broad/602221-20260417-2346-S21-B-Z0317-CTGCGCAGCATCCTGAT-prod-cram-11-CTGCGCAGCATCCTGAT-PF-UG-ULTIMA/align/ug/na/logs/dedupe.na.602221-20260417-2346-S21-B-Z0317-CTGCGCAGCATCCTGAT-prod-cram-11-CTGCGCAGCATCCTGAT-PF-UG-ULTIMA.ug.log

        # Use relative symlinks so the tree is relocatable
        ln -sfn "$(realpath --relative-to=$(dirname results/day/hg38_broad/602221-20260417-2346-S21-B-Z0317-CTGCGCAGCATCCTGAT-prod-cram-11-CTGCGCAGCATCCTGAT-PF-UG-ULTIMA/align/ug/na/602221-20260417-2346-S21-B-Z0317-CTGCGCAGCATCCTGAT-prod-cram-11-CTGCGCAGCATCCTGAT-PF-UG-ULTIMA.ug.na.cram) results/day/hg38_broad/602221-20260417-2346-S21-B-Z0317-CTGCGCAGCATCCTGAT-prod-cram-11-CTGCGCAGCATCCTGAT-PF-UG-ULTIMA/align/ug/602221-20260417-2346-S21-B-Z0317-CTGCGCAGCATCCTGAT-prod-cram-11-CTGCGCAGCATCCTGAT-PF-UG-ULTIMA.cram)" results/day/hg38_broad/602221-20260417-2346-S21-B-Z0317-CTGCGCAGCATCCTGAT-prod-cram-11-CTGCGCAGCATCCTGAT-PF-UG-ULTIMA/align/ug/na/602221-20260417-2346-S21-B-Z0317-CTGCGCAGCATCCTGAT-prod-cram-11-CTGCGCAGCATCCTGAT-PF-UG-ULTIMA.ug.na.cram >> results/day/hg38_broad/602221-20260417-2346-S21-B-Z0317-CTGCGCAGCATCCTGAT-prod-cram-11-CTGCGCAGCATCCTGAT-PF-UG-ULTIMA/align/ug/na/logs/dedupe.na.602221-20260417-2346-S21-B-Z0317-CTGCGCAGCATCCTGAT-prod-cram-11-CTGCGCAGCATCCTGAT-PF-UG-ULTIMA.ug.log 2>&1
        ln -sfn "$(realpath --relative-to=$(dirname results/day/hg38_broad/602221-20260417-2346-S21-B-Z0317-CTGCGCAGCATCCTGAT-prod-cram-11-CTGCGCAGCATCCTGAT-PF-UG-ULTIMA/align/ug/na/602221-20260417-2346-S21-B-Z0317-CTGCGCAGCATCCTGAT-prod-cram-11-CTGCGCAGCATCCTGAT-PF-UG-ULTIMA.ug.na.cram.crai) results/day/hg38_broad/602221-20260417-2346-S21-B-Z0317-CTGCGCAGCATCCTGAT-prod-cram-11-CTGCGCAGCATCCTGAT-PF-UG-ULTIMA/align/ug/602221-20260417-2346-S21-B-Z0317-CTGCGCAGCATCCTGAT-prod-cram-11-CTGCGCAGCATCCTGAT-PF-UG-ULTIMA.cram.crai)" results/day/hg38_broad/602221-20260417-2346-S21-B-Z0317-CTGCGCAGCATCCTGAT-prod-cram-11-CTGCGCAGCATCCTGAT-PF-UG-ULTIMA/align/ug/na/602221-20260417-2346-S21-B-Z0317-CTGCGCAGCATCCTGAT-prod-cram-11-CTGCGCAGCATCCTGAT-PF-UG-ULTIMA.ug.na.cram.crai >> results/day/hg38_broad/602221-20260417-2346-S21-B-Z0317-CTGCGCAGCATCCTGAT-prod-cram-11-CTGCGCAGCATCCTGAT-PF-UG-ULTIMA/align/ug/na/logs/dedupe.na.602221-20260417-2346-S21-B-Z0317-CTGCGCAGCATCCTGAT-prod-cram-11-CTGCGCAGCATCCTGAT-PF-UG-ULTIMA.ug.log 2>&1

        echo "Symlinked results/day/hg38_broad/602221-20260417-2346-S21-B-Z0317-CTGCGCAGCATCCTGAT-prod-cram-11-CTGCGCAGCATCCTGAT-PF-UG-ULTIMA/align/ug/602221-20260417-2346-S21-B-Z0317-CTGCGCAGCATCCTGAT-prod-cram-11-CTGCGCAGCATCCTGAT-PF-UG-ULTIMA.cram → results/day/hg38_broad/602221-20260417-2346-S21-B-Z0317-CTGCGCAGCATCCTGAT-prod-cram-11-CTGCGCAGCATCCTGAT-PF-UG-ULTIMA/align/ug/na/602221-20260417-2346-S21-B-Z0317-CTGCGCAGCATCCTGAT-prod-cram-11-CTGCGCAGCATCCTGAT-PF-UG-ULTIMA.ug.na.cram" >> results/day/hg38_broad/602221-20260417-2346-S21-B-Z0317-CTGCGCAGCATCCTGAT-prod-cram-11-CTGCGCAGCATCCTGAT-PF-UG-ULTIMA/align/ug/na/logs/dedupe.na.602221-20260417-2346-S21-B-Z0317-CTGCGCAGCATCCTGAT-prod-cram-11-CTGCGCAGCATCCTGAT-PF-UG-ULTIMA.ug.log 2>&1
        echo "Symlinked results/day/hg38_broad/602221-20260417-2346-S21-B-Z0317-CTGCGCAGCATCCTGAT-prod-cram-11-CTGCGCAGCATCCTGAT-PF-UG-ULTIMA/align/ug/602221-20260417-2346-S21-B-Z0317-CTGCGCAGCATCCTGAT-prod-cram-11-CTGCGCAGCATCCTGAT-PF-UG-ULTIMA.cram.crai → results/day/hg38_broad/602221-20260417-2346-S21-B-Z0317-CTGCGCAGCATCCTGAT-prod-cram-11-CTGCGCAGCATCCTGAT-PF-UG-ULTIMA/align/ug/na/602221-20260417-2346-S21-B-Z0317-CTGCGCAGCATCCTGAT-prod-cram-11-CTGCGCAGCATCCTGAT-PF-UG-ULTIMA.ug.na.cram.crai" >> results/day/hg38_broad/602221-20260417-2346-S21-B-Z0317-CTGCGCAGCATCCTGAT-prod-cram-11-CTGCGCAGCATCCTGAT-PF-UG-ULTIMA/align/ug/na/logs/dedupe.na.602221-20260417-2346-S21-B-Z0317-CTGCGCAGCATCCTGAT-prod-cram-11-CTGCGCAGCATCCTGAT-PF-UG-ULTIMA.ug.log 2>&1
        
Submitted job 45 with external jobid '1893'.

[Sat Apr 25 09:08:43 2026]
rule no_dedup_cram:
    input: results/day/hg38_broad/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA/align/ug/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA.cram, results/day/hg38_broad/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA/align/ug/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA.cram.crai
    output: results/day/hg38_broad/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA/align/ug/na/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA.ug.na.cram, results/day/hg38_broad/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA/align/ug/na/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA.ug.na.cram.crai
    log: results/day/hg38_broad/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA/align/ug/na/logs/dedupe.na.602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA.ug.log
    jobid: 53
    benchmark: results/day/hg38_broad/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA/benchmarks/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA.ug.na.mrkdup.bench.tsv
    reason: Missing output files: results/day/hg38_broad/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA/align/ug/na/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA.ug.na.cram.crai, results/day/hg38_broad/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA/align/ug/na/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA.ug.na.cram; Input files updated by another job: results/day/hg38_broad/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA/align/ug/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA.cram.crai, results/day/hg38_broad/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA/align/ug/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA.cram
    wildcards: sample=602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA, alnr=ug
    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/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA/align/ug/na/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA.ug.na.cram)
        touch results/day/hg38_broad/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA/align/ug/na/logs/dedupe.na.602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA.ug.log

        # Use relative symlinks so the tree is relocatable
        ln -sfn "$(realpath --relative-to=$(dirname results/day/hg38_broad/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA/align/ug/na/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA.ug.na.cram) results/day/hg38_broad/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA/align/ug/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA.cram)" results/day/hg38_broad/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA/align/ug/na/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA.ug.na.cram >> results/day/hg38_broad/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA/align/ug/na/logs/dedupe.na.602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA.ug.log 2>&1
        ln -sfn "$(realpath --relative-to=$(dirname results/day/hg38_broad/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA/align/ug/na/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA.ug.na.cram.crai) results/day/hg38_broad/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA/align/ug/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA.cram.crai)" results/day/hg38_broad/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA/align/ug/na/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA.ug.na.cram.crai >> results/day/hg38_broad/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA/align/ug/na/logs/dedupe.na.602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA.ug.log 2>&1

        echo "Symlinked results/day/hg38_broad/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA/align/ug/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA.cram → results/day/hg38_broad/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA/align/ug/na/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA.ug.na.cram" >> results/day/hg38_broad/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA/align/ug/na/logs/dedupe.na.602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA.ug.log 2>&1
        echo "Symlinked results/day/hg38_broad/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA/align/ug/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA.cram.crai → results/day/hg38_broad/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA/align/ug/na/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA.ug.na.cram.crai" >> results/day/hg38_broad/602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA/align/ug/na/logs/dedupe.na.602221-20260417-2346-S2b-B-Z0320-CAGTGCGACAATGAT-prod-cram-13-CAGTGCGACAATGAT-PF-UG-ULTIMA.ug.log 2>&1
        
Submitted job 53 with external jobid '1894'.
[Sat Apr 25 09:08:53 2026]
Finished job 65.
17 of 67 steps (25%) done
Select jobs to execute...

[Sat Apr 25 09:08:53 2026]
rule alignstats:
    input: results/day/hg38_broad/602221-20260417-2346-S8-B-Z0308-CAGAGCGCCGCAGAT-prod-cram-16-CAGAGCGCCGCAGAT-PF-UG-ULTIMA/align/ug/na/602221-20260417-2346-S8-B-Z0308-CAGAGCGCCGCAGAT-prod-cram-16-CAGAGCGCCGCAGAT-PF-UG-ULTIMA.ug.na.cram, results/day/hg38_broad/602221-20260417-2346-S8-B-Z0308-CAGAGCGCCGCAGAT-prod-cram-16-CAGAGCGCCGCAGAT-PF-UG-ULTIMA/align/ug/na/602221-20260417-2346-S8-B-Z0308-CAGAGCGCCGCAGAT-prod-cram-16-CAGAGCGCCGCAGAT-PF-UG-ULTIMA.ug.na.cram.crai
    output: results/day/hg38_broad/602221-20260417-2346-S8-B-Z0308-CAGAGCGCCGCAGAT-prod-cram-16-CAGAGCGCCGCAGAT-PF-UG-ULTIMA/align/ug/na/alignqc/alignstats/602221-20260417-2346-S8-B-Z0308-CAGAGCGCCGCAGAT-prod-cram-16-CAGAGCGCCGCAGAT-PF-UG-ULTIMA.ug.na.alignstats.json
    log: results/day/hg38_broad/602221-20260417-2346-S8-B-Z0308-CAGAGCGCCGCAGAT-prod-cram-16-CAGAGCGCCGCAGAT-PF-UG-ULTIMA/align/ug/na/alignqc/alignstats/logs/602221-20260417-2346-S8-B-Z0308-CAGAGCGCCGCAGAT-prod-cram-16-CAGAGCGCCGCAGAT-PF-UG-ULTIMA.ug.na.alignstats.log
    jobid: 64
    benchmark: results/day/hg38_broad/602221-20260417-2346-S8-B-Z0308-CAGAGCGCCGCAGAT-prod-cram-16-CAGAGCGCCGCAGAT-PF-UG-ULTIMA/benchmarks/602221-20260417-2346-S8-B-Z0308-CAGAGCGCCGCAGAT-prod-cram-16-CAGAGCGCCGCAGAT-PF-UG-ULTIMA.ug.na.alignstats.bench.tsv
    reason: Missing output files: results/day/hg38_broad/602221-20260417-2346-S8-B-Z0308-CAGAGCGCCGCAGAT-prod-cram-16-CAGAGCGCCGCAGAT-PF-UG-ULTIMA/align/ug/na/alignqc/alignstats/602221-20260417-2346-S8-B-Z0308-CAGAGCGCCGCAGAT-prod-cram-16-CAGAGCGCCGCAGAT-PF-UG-ULTIMA.ug.na.alignstats.json; Input files updated by another job: results/day/hg38_broad/602221-20260417-2346-S8-B-Z0308-CAGAGCGCCGCAGAT-prod-cram-16-CAGAGCGCCGCAGAT-PF-UG-ULTIMA/align/ug/na/602221-20260417-2346-S8-B-Z0308-CAGAGCGCCGCAGAT-prod-cram-16-CAGAGCGCCGCAGAT-PF-UG-ULTIMA.ug.na.cram, results/day/hg38_broad/602221-20260417-2346-S8-B-Z0308-CAGAGCGCCGCAGAT-prod-cram-16-CAGAGCGCCGCAGAT-PF-UG-ULTIMA/align/ug/na/602221-20260417-2346-S8-B-Z0308-CAGAGCGCCGCAGAT-prod-cram-16-CAGAGCGCCGCAGAT-PF-UG-ULTIMA.ug.na.cram.crai
    wildcards: sample=602221-20260417-2346-S8-B-Z0308-CAGAGCGCCGCAGAT-prod-cram-16-CAGAGCGCCGCAGAT-PF-UG-ULTIMA, alnr=ug, 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/602221-20260417-2346-S8-B-Z0308-CAGAGCGCCGCAGAT-prod-cram-16-CAGAGCGCCGCAGAT-PF-UG-ULTIMA/align/ug/na/602221-20260417-2346-S8-B-Z0308-CAGAGCGCCGCAGAT-prod-cram-16-CAGAGCGCCGCAGAT-PF-UG-ULTIMA.ug.na.cram -T /fsx/data/genomic_data/organism_references/H_sapiens/hg38_broad/Homo_sapiens_assembly38.fasta -o results/day/hg38_broad/602221-20260417-2346-S8-B-Z0308-CAGAGCGCCGCAGAT-prod-cram-16-CAGAGCGCCGCAGAT-PF-UG-ULTIMA/align/ug/na/alignqc/alignstats/602221-20260417-2346-S8-B-Z0308-CAGAGCGCCGCAGAT-prod-cram-16-CAGAGCGCCGCAGAT-PF-UG-ULTIMA.ug.na.alignstats.json  -j cram -v -P 96 -p 96 > results/day/hg38_broad/602221-20260417-2346-S8-B-Z0308-CAGAGCGCCGCAGAT-prod-cram-16-CAGAGCGCCGCAGAT-PF-UG-ULTIMA/align/ug/na/alignqc/alignstats/logs/602221-20260417-2346-S8-B-Z0308-CAGAGCGCCGCAGAT-prod-cram-16-CAGAGCGCCGCAGAT-PF-UG-ULTIMA.ug.na.alignstats.log;
Submitted job 64 with external jobid '1905'.
[Sat Apr 25 09:08:53 2026]
Finished job 29.
18 of 67 steps (27%) done
Select jobs to execute...

[Sat Apr 25 09:08:53 2026]
rule alignstats:
    input: results/day/hg38_broad/602221-20260417-2346-S16-B-Z0315-CACGAGCGCAATGAT-prod-cram-7-CACGAGCGCAATGAT-PF-UG-ULTIMA/align/ug/na/602221-20260417-2346-S16-B-Z0315-CACGAGCGCAATGAT-prod-cram-7-CACGAGCGCAATGAT-PF-UG-ULTIMA.ug.na.cram, results/day/hg38_broad/602221-20260417-2346-S16-B-Z0315-CACGAGCGCAATGAT-prod-cram-7-CACGAGCGCAATGAT-PF-UG-ULTIMA/align/ug/na/602221-20260417-2346-S16-B-Z0315-CACGAGCGCAATGAT-prod-cram-7-CACGAGCGCAATGAT-PF-UG-ULTIMA.ug.na.cram.crai
    output: results/day/hg38_broad/602221-20260417-2346-S16-B-Z0315-CACGAGCGCAATGAT-prod-cram-7-CACGAGCGCAATGAT-PF-UG-ULTIMA/align/ug/na/alignqc/alignstats/602221-20260417-2346-S16-B-Z0315-CACGAGCGCAATGAT-prod-cram-7-CACGAGCGCAATGAT-PF-UG-ULTIMA.ug.na.alignstats.json
    log: results/day/hg38_broad/602221-20260417-2346-S16-B-Z0315-CACGAGCGCAATGAT-prod-cram-7-CACGAGCGCAATGAT-PF-UG-ULTIMA/align/ug/na/alignqc/alignstats/logs/602221-20260417-2346-S16-B-Z0315-CACGAGCGCAATGAT-prod-cram-7-CACGAGCGCAATGAT-PF-UG-ULTIMA.ug.na.alignstats.log
    jobid: 28
    benchmark: results/day/hg38_broad/602221-20260417-2346-S16-B-Z0315-CACGAGCGCAATGAT-prod-cram-7-CACGAGCGCAATGAT-PF-UG-ULTIMA/benchmarks/602221-20260417-2346-S16-B-Z0315-CACGAGCGCAATGAT-prod-cram-7-CACGAGCGCAATGAT-PF-UG-ULTIMA.ug.na.alignstats.bench.tsv
    reason: Missing output files: results/day/hg38_broad/602221-20260417-2346-S16-B-Z0315-CACGAGCGCAATGAT-prod-cram-7-CACGAGCGCAATGAT-PF-UG-ULTIMA/align/ug/na/alignqc/alignstats/602221-20260417-2346-S16-B-Z0315-CACGAGCGCAATGAT-prod-cram-7-CACGAGCGCAATGAT-PF-UG-ULTIMA.ug.na.alignstats.json; Input files updated by another job: results/day/hg38_broad/602221-20260417-2346-S16-B-Z0315-CACGAGCGCAATGAT-prod-cram-7-CACGAGCGCAATGAT-PF-UG-ULTIMA/align/ug/na/602221-20260417-2346-S16-B-Z0315-CACGAGCGCAATGAT-prod-cram-7-CACGAGCGCAATGAT-PF-UG-ULTIMA.ug.na.cram.crai, results/day/hg38_broad/602221-20260417-2346-S16-B-Z0315-CACGAGCGCAATGAT-prod-cram-7-CACGAGCGCAATGAT-PF-UG-ULTIMA/align/ug/na/602221-20260417-2346-S16-B-Z0315-CACGAGCGCAATGAT-prod-cram-7-CACGAGCGCAATGAT-PF-UG-ULTIMA.ug.na.cram
    wildcards: sample=602221-20260417-2346-S16-B-Z0315-CACGAGCGCAATGAT-prod-cram-7-CACGAGCGCAATGAT-PF-UG-ULTIMA, alnr=ug, 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/602221-20260417-2346-S16-B-Z0315-CACGAGCGCAATGAT-prod-cram-7-CACGAGCGCAATGAT-PF-UG-ULTIMA/align/ug/na/602221-20260417-2346-S16-B-Z0315-CACGAGCGCAATGAT-prod-cram-7-CACGAGCGCAATGAT-PF-UG-ULTIMA.ug.na.cram -T /fsx/data/genomic_data/organism_references/H_sapiens/hg38_broad/Homo_sapiens_assembly38.fasta -o results/day/hg38_broad/602221-20260417-2346-S16-B-Z0315-CACGAGCGCAATGAT-prod-cram-7-CACGAGCGCAATGAT-PF-UG-ULTIMA/align/ug/na/alignqc/alignstats/602221-20260417-2346-S16-B-Z0315-CACGAGCGCAATGAT-prod-cram-7-CACGAGCGCAATGAT-PF-UG-ULTIMA.ug.na.alignstats.json  -j cram -v -P 96 -p 96 > results/day/hg38_broad/602221-20260417-2346-S16-B-Z0315-CACGAGCGCAATGAT-prod-cram-7-CACGAGCGCAATGAT-PF-UG-ULTIMA/align/ug/na/alignqc/alignstats/logs/602221-20260417-2346-S16-B-Z0315-CACGAGCGCAATGAT-prod-cram-7-CACGAGCGCAATGAT-PF-UG-ULTIMA.ug.na.alignstats.log;
Submitted job 28 with external jobid '1906'.
