DAY-EC activated.
DAY-EC activated.
22 of 67 steps (33%) done
Select jobs to execute...

[Sat Apr 25 09:33:49 2026]
rule alignstats:
    input: results/day/hg38_broad/602220-20260417-2047-S17-A-Z0293-CATGTGAGCGGTGAT-prod-cram-8-CATGTGAGCGGTGAT-PF-UG-ULTIMA/align/ug/na/602220-20260417-2047-S17-A-Z0293-CATGTGAGCGGTGAT-prod-cram-8-CATGTGAGCGGTGAT-PF-UG-ULTIMA.ug.na.cram, results/day/hg38_broad/602220-20260417-2047-S17-A-Z0293-CATGTGAGCGGTGAT-prod-cram-8-CATGTGAGCGGTGAT-PF-UG-ULTIMA/align/ug/na/602220-20260417-2047-S17-A-Z0293-CATGTGAGCGGTGAT-prod-cram-8-CATGTGAGCGGTGAT-PF-UG-ULTIMA.ug.na.cram.crai
    output: results/day/hg38_broad/602220-20260417-2047-S17-A-Z0293-CATGTGAGCGGTGAT-prod-cram-8-CATGTGAGCGGTGAT-PF-UG-ULTIMA/align/ug/na/alignqc/alignstats/602220-20260417-2047-S17-A-Z0293-CATGTGAGCGGTGAT-prod-cram-8-CATGTGAGCGGTGAT-PF-UG-ULTIMA.ug.na.alignstats.json
    log: results/day/hg38_broad/602220-20260417-2047-S17-A-Z0293-CATGTGAGCGGTGAT-prod-cram-8-CATGTGAGCGGTGAT-PF-UG-ULTIMA/align/ug/na/alignqc/alignstats/logs/602220-20260417-2047-S17-A-Z0293-CATGTGAGCGGTGAT-prod-cram-8-CATGTGAGCGGTGAT-PF-UG-ULTIMA.ug.na.alignstats.log
    jobid: 32
    benchmark: results/day/hg38_broad/602220-20260417-2047-S17-A-Z0293-CATGTGAGCGGTGAT-prod-cram-8-CATGTGAGCGGTGAT-PF-UG-ULTIMA/benchmarks/602220-20260417-2047-S17-A-Z0293-CATGTGAGCGGTGAT-prod-cram-8-CATGTGAGCGGTGAT-PF-UG-ULTIMA.ug.na.alignstats.bench.tsv
    reason: Missing output files: results/day/hg38_broad/602220-20260417-2047-S17-A-Z0293-CATGTGAGCGGTGAT-prod-cram-8-CATGTGAGCGGTGAT-PF-UG-ULTIMA/align/ug/na/alignqc/alignstats/602220-20260417-2047-S17-A-Z0293-CATGTGAGCGGTGAT-prod-cram-8-CATGTGAGCGGTGAT-PF-UG-ULTIMA.ug.na.alignstats.json; Input files updated by another job: results/day/hg38_broad/602220-20260417-2047-S17-A-Z0293-CATGTGAGCGGTGAT-prod-cram-8-CATGTGAGCGGTGAT-PF-UG-ULTIMA/align/ug/na/602220-20260417-2047-S17-A-Z0293-CATGTGAGCGGTGAT-prod-cram-8-CATGTGAGCGGTGAT-PF-UG-ULTIMA.ug.na.cram, results/day/hg38_broad/602220-20260417-2047-S17-A-Z0293-CATGTGAGCGGTGAT-prod-cram-8-CATGTGAGCGGTGAT-PF-UG-ULTIMA/align/ug/na/602220-20260417-2047-S17-A-Z0293-CATGTGAGCGGTGAT-prod-cram-8-CATGTGAGCGGTGAT-PF-UG-ULTIMA.ug.na.cram.crai
    wildcards: sample=602220-20260417-2047-S17-A-Z0293-CATGTGAGCGGTGAT-prod-cram-8-CATGTGAGCGGTGAT-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/602220-20260417-2047-S17-A-Z0293-CATGTGAGCGGTGAT-prod-cram-8-CATGTGAGCGGTGAT-PF-UG-ULTIMA/align/ug/na/602220-20260417-2047-S17-A-Z0293-CATGTGAGCGGTGAT-prod-cram-8-CATGTGAGCGGTGAT-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/602220-20260417-2047-S17-A-Z0293-CATGTGAGCGGTGAT-prod-cram-8-CATGTGAGCGGTGAT-PF-UG-ULTIMA/align/ug/na/alignqc/alignstats/602220-20260417-2047-S17-A-Z0293-CATGTGAGCGGTGAT-prod-cram-8-CATGTGAGCGGTGAT-PF-UG-ULTIMA.ug.na.alignstats.json  -j cram -v -P 96 -p 96 > results/day/hg38_broad/602220-20260417-2047-S17-A-Z0293-CATGTGAGCGGTGAT-prod-cram-8-CATGTGAGCGGTGAT-PF-UG-ULTIMA/align/ug/na/alignqc/alignstats/logs/602220-20260417-2047-S17-A-Z0293-CATGTGAGCGGTGAT-prod-cram-8-CATGTGAGCGGTGAT-PF-UG-ULTIMA.ug.na.alignstats.log;
Submitted job 32 with external jobid '2123'.

[Sat Apr 25 09:33:49 2026]
rule alignstats:
    input: results/day/hg38_broad/602220-20260417-2047-S15-A-Z0298-CAAGACTGATATGAT-prod-cram-6-CAAGACTGATATGAT-PF-UG-ULTIMA/align/ug/na/602220-20260417-2047-S15-A-Z0298-CAAGACTGATATGAT-prod-cram-6-CAAGACTGATATGAT-PF-UG-ULTIMA.ug.na.cram, results/day/hg38_broad/602220-20260417-2047-S15-A-Z0298-CAAGACTGATATGAT-prod-cram-6-CAAGACTGATATGAT-PF-UG-ULTIMA/align/ug/na/602220-20260417-2047-S15-A-Z0298-CAAGACTGATATGAT-prod-cram-6-CAAGACTGATATGAT-PF-UG-ULTIMA.ug.na.cram.crai
    output: results/day/hg38_broad/602220-20260417-2047-S15-A-Z0298-CAAGACTGATATGAT-prod-cram-6-CAAGACTGATATGAT-PF-UG-ULTIMA/align/ug/na/alignqc/alignstats/602220-20260417-2047-S15-A-Z0298-CAAGACTGATATGAT-prod-cram-6-CAAGACTGATATGAT-PF-UG-ULTIMA.ug.na.alignstats.json
    log: results/day/hg38_broad/602220-20260417-2047-S15-A-Z0298-CAAGACTGATATGAT-prod-cram-6-CAAGACTGATATGAT-PF-UG-ULTIMA/align/ug/na/alignqc/alignstats/logs/602220-20260417-2047-S15-A-Z0298-CAAGACTGATATGAT-prod-cram-6-CAAGACTGATATGAT-PF-UG-ULTIMA.ug.na.alignstats.log
    jobid: 24
    benchmark: results/day/hg38_broad/602220-20260417-2047-S15-A-Z0298-CAAGACTGATATGAT-prod-cram-6-CAAGACTGATATGAT-PF-UG-ULTIMA/benchmarks/602220-20260417-2047-S15-A-Z0298-CAAGACTGATATGAT-prod-cram-6-CAAGACTGATATGAT-PF-UG-ULTIMA.ug.na.alignstats.bench.tsv
    reason: Missing output files: results/day/hg38_broad/602220-20260417-2047-S15-A-Z0298-CAAGACTGATATGAT-prod-cram-6-CAAGACTGATATGAT-PF-UG-ULTIMA/align/ug/na/alignqc/alignstats/602220-20260417-2047-S15-A-Z0298-CAAGACTGATATGAT-prod-cram-6-CAAGACTGATATGAT-PF-UG-ULTIMA.ug.na.alignstats.json; Input files updated by another job: results/day/hg38_broad/602220-20260417-2047-S15-A-Z0298-CAAGACTGATATGAT-prod-cram-6-CAAGACTGATATGAT-PF-UG-ULTIMA/align/ug/na/602220-20260417-2047-S15-A-Z0298-CAAGACTGATATGAT-prod-cram-6-CAAGACTGATATGAT-PF-UG-ULTIMA.ug.na.cram.crai, results/day/hg38_broad/602220-20260417-2047-S15-A-Z0298-CAAGACTGATATGAT-prod-cram-6-CAAGACTGATATGAT-PF-UG-ULTIMA/align/ug/na/602220-20260417-2047-S15-A-Z0298-CAAGACTGATATGAT-prod-cram-6-CAAGACTGATATGAT-PF-UG-ULTIMA.ug.na.cram
    wildcards: sample=602220-20260417-2047-S15-A-Z0298-CAAGACTGATATGAT-prod-cram-6-CAAGACTGATATGAT-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/602220-20260417-2047-S15-A-Z0298-CAAGACTGATATGAT-prod-cram-6-CAAGACTGATATGAT-PF-UG-ULTIMA/align/ug/na/602220-20260417-2047-S15-A-Z0298-CAAGACTGATATGAT-prod-cram-6-CAAGACTGATATGAT-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/602220-20260417-2047-S15-A-Z0298-CAAGACTGATATGAT-prod-cram-6-CAAGACTGATATGAT-PF-UG-ULTIMA/align/ug/na/alignqc/alignstats/602220-20260417-2047-S15-A-Z0298-CAAGACTGATATGAT-prod-cram-6-CAAGACTGATATGAT-PF-UG-ULTIMA.ug.na.alignstats.json  -j cram -v -P 96 -p 96 > results/day/hg38_broad/602220-20260417-2047-S15-A-Z0298-CAAGACTGATATGAT-prod-cram-6-CAAGACTGATATGAT-PF-UG-ULTIMA/align/ug/na/alignqc/alignstats/logs/602220-20260417-2047-S15-A-Z0298-CAAGACTGATATGAT-prod-cram-6-CAAGACTGATATGAT-PF-UG-ULTIMA.ug.na.alignstats.log;
Submitted job 24 with external jobid '2124'.

[Sat Apr 25 09:33:49 2026]
rule alignstats:
    input: results/day/hg38_broad/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA/align/ug/na/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA.ug.na.cram, results/day/hg38_broad/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA/align/ug/na/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA.ug.na.cram.crai
    output: results/day/hg38_broad/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA/align/ug/na/alignqc/alignstats/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA.ug.na.alignstats.json
    log: results/day/hg38_broad/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA/align/ug/na/alignqc/alignstats/logs/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA.ug.na.alignstats.log
    jobid: 8
    benchmark: results/day/hg38_broad/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA/benchmarks/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA.ug.na.alignstats.bench.tsv
    reason: Missing output files: results/day/hg38_broad/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA/align/ug/na/alignqc/alignstats/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA.ug.na.alignstats.json; Input files updated by another job: results/day/hg38_broad/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA/align/ug/na/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA.ug.na.cram.crai, results/day/hg38_broad/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA/align/ug/na/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA.ug.na.cram
    wildcards: sample=602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-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/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA/align/ug/na/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-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/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA/align/ug/na/alignqc/alignstats/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA.ug.na.alignstats.json  -j cram -v -P 96 -p 96 > results/day/hg38_broad/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA/align/ug/na/alignqc/alignstats/logs/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA.ug.na.alignstats.log;
Submitted job 8 with external jobid '2125'.

[Sat Apr 25 09:33:49 2026]
rule alignstats:
    input: results/day/hg38_broad/602220-20260417-2047-S13-A-Z0296-CATCTATCAGGCGAT-prod-cram-4-CATCTATCAGGCGAT-PF-UG-ULTIMA/align/ug/na/602220-20260417-2047-S13-A-Z0296-CATCTATCAGGCGAT-prod-cram-4-CATCTATCAGGCGAT-PF-UG-ULTIMA.ug.na.cram, results/day/hg38_broad/602220-20260417-2047-S13-A-Z0296-CATCTATCAGGCGAT-prod-cram-4-CATCTATCAGGCGAT-PF-UG-ULTIMA/align/ug/na/602220-20260417-2047-S13-A-Z0296-CATCTATCAGGCGAT-prod-cram-4-CATCTATCAGGCGAT-PF-UG-ULTIMA.ug.na.cram.crai
    output: results/day/hg38_broad/602220-20260417-2047-S13-A-Z0296-CATCTATCAGGCGAT-prod-cram-4-CATCTATCAGGCGAT-PF-UG-ULTIMA/align/ug/na/alignqc/alignstats/602220-20260417-2047-S13-A-Z0296-CATCTATCAGGCGAT-prod-cram-4-CATCTATCAGGCGAT-PF-UG-ULTIMA.ug.na.alignstats.json
    log: results/day/hg38_broad/602220-20260417-2047-S13-A-Z0296-CATCTATCAGGCGAT-prod-cram-4-CATCTATCAGGCGAT-PF-UG-ULTIMA/align/ug/na/alignqc/alignstats/logs/602220-20260417-2047-S13-A-Z0296-CATCTATCAGGCGAT-prod-cram-4-CATCTATCAGGCGAT-PF-UG-ULTIMA.ug.na.alignstats.log
    jobid: 16
    benchmark: results/day/hg38_broad/602220-20260417-2047-S13-A-Z0296-CATCTATCAGGCGAT-prod-cram-4-CATCTATCAGGCGAT-PF-UG-ULTIMA/benchmarks/602220-20260417-2047-S13-A-Z0296-CATCTATCAGGCGAT-prod-cram-4-CATCTATCAGGCGAT-PF-UG-ULTIMA.ug.na.alignstats.bench.tsv
    reason: Missing output files: results/day/hg38_broad/602220-20260417-2047-S13-A-Z0296-CATCTATCAGGCGAT-prod-cram-4-CATCTATCAGGCGAT-PF-UG-ULTIMA/align/ug/na/alignqc/alignstats/602220-20260417-2047-S13-A-Z0296-CATCTATCAGGCGAT-prod-cram-4-CATCTATCAGGCGAT-PF-UG-ULTIMA.ug.na.alignstats.json; Input files updated by another job: results/day/hg38_broad/602220-20260417-2047-S13-A-Z0296-CATCTATCAGGCGAT-prod-cram-4-CATCTATCAGGCGAT-PF-UG-ULTIMA/align/ug/na/602220-20260417-2047-S13-A-Z0296-CATCTATCAGGCGAT-prod-cram-4-CATCTATCAGGCGAT-PF-UG-ULTIMA.ug.na.cram.crai, results/day/hg38_broad/602220-20260417-2047-S13-A-Z0296-CATCTATCAGGCGAT-prod-cram-4-CATCTATCAGGCGAT-PF-UG-ULTIMA/align/ug/na/602220-20260417-2047-S13-A-Z0296-CATCTATCAGGCGAT-prod-cram-4-CATCTATCAGGCGAT-PF-UG-ULTIMA.ug.na.cram
    wildcards: sample=602220-20260417-2047-S13-A-Z0296-CATCTATCAGGCGAT-prod-cram-4-CATCTATCAGGCGAT-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/602220-20260417-2047-S13-A-Z0296-CATCTATCAGGCGAT-prod-cram-4-CATCTATCAGGCGAT-PF-UG-ULTIMA/align/ug/na/602220-20260417-2047-S13-A-Z0296-CATCTATCAGGCGAT-prod-cram-4-CATCTATCAGGCGAT-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/602220-20260417-2047-S13-A-Z0296-CATCTATCAGGCGAT-prod-cram-4-CATCTATCAGGCGAT-PF-UG-ULTIMA/align/ug/na/alignqc/alignstats/602220-20260417-2047-S13-A-Z0296-CATCTATCAGGCGAT-prod-cram-4-CATCTATCAGGCGAT-PF-UG-ULTIMA.ug.na.alignstats.json  -j cram -v -P 96 -p 96 > results/day/hg38_broad/602220-20260417-2047-S13-A-Z0296-CATCTATCAGGCGAT-prod-cram-4-CATCTATCAGGCGAT-PF-UG-ULTIMA/align/ug/na/alignqc/alignstats/logs/602220-20260417-2047-S13-A-Z0296-CATCTATCAGGCGAT-prod-cram-4-CATCTATCAGGCGAT-PF-UG-ULTIMA.ug.na.alignstats.log;
Submitted job 16 with external jobid '2126'.

[Sat Apr 25 09:33:49 2026]
rule alignstats:
    input: results/day/hg38_broad/602220-20260417-2047-S16-A-Z0299-CATGCGGAGTGAGAT-prod-cram-7-CATGCGGAGTGAGAT-PF-UG-ULTIMA/align/ug/na/602220-20260417-2047-S16-A-Z0299-CATGCGGAGTGAGAT-prod-cram-7-CATGCGGAGTGAGAT-PF-UG-ULTIMA.ug.na.cram, results/day/hg38_broad/602220-20260417-2047-S16-A-Z0299-CATGCGGAGTGAGAT-prod-cram-7-CATGCGGAGTGAGAT-PF-UG-ULTIMA/align/ug/na/602220-20260417-2047-S16-A-Z0299-CATGCGGAGTGAGAT-prod-cram-7-CATGCGGAGTGAGAT-PF-UG-ULTIMA.ug.na.cram.crai
    output: results/day/hg38_broad/602220-20260417-2047-S16-A-Z0299-CATGCGGAGTGAGAT-prod-cram-7-CATGCGGAGTGAGAT-PF-UG-ULTIMA/align/ug/na/alignqc/alignstats/602220-20260417-2047-S16-A-Z0299-CATGCGGAGTGAGAT-prod-cram-7-CATGCGGAGTGAGAT-PF-UG-ULTIMA.ug.na.alignstats.json
    log: results/day/hg38_broad/602220-20260417-2047-S16-A-Z0299-CATGCGGAGTGAGAT-prod-cram-7-CATGCGGAGTGAGAT-PF-UG-ULTIMA/align/ug/na/alignqc/alignstats/logs/602220-20260417-2047-S16-A-Z0299-CATGCGGAGTGAGAT-prod-cram-7-CATGCGGAGTGAGAT-PF-UG-ULTIMA.ug.na.alignstats.log
    jobid: 28
    benchmark: results/day/hg38_broad/602220-20260417-2047-S16-A-Z0299-CATGCGGAGTGAGAT-prod-cram-7-CATGCGGAGTGAGAT-PF-UG-ULTIMA/benchmarks/602220-20260417-2047-S16-A-Z0299-CATGCGGAGTGAGAT-prod-cram-7-CATGCGGAGTGAGAT-PF-UG-ULTIMA.ug.na.alignstats.bench.tsv
    reason: Missing output files: results/day/hg38_broad/602220-20260417-2047-S16-A-Z0299-CATGCGGAGTGAGAT-prod-cram-7-CATGCGGAGTGAGAT-PF-UG-ULTIMA/align/ug/na/alignqc/alignstats/602220-20260417-2047-S16-A-Z0299-CATGCGGAGTGAGAT-prod-cram-7-CATGCGGAGTGAGAT-PF-UG-ULTIMA.ug.na.alignstats.json; Input files updated by another job: results/day/hg38_broad/602220-20260417-2047-S16-A-Z0299-CATGCGGAGTGAGAT-prod-cram-7-CATGCGGAGTGAGAT-PF-UG-ULTIMA/align/ug/na/602220-20260417-2047-S16-A-Z0299-CATGCGGAGTGAGAT-prod-cram-7-CATGCGGAGTGAGAT-PF-UG-ULTIMA.ug.na.cram, results/day/hg38_broad/602220-20260417-2047-S16-A-Z0299-CATGCGGAGTGAGAT-prod-cram-7-CATGCGGAGTGAGAT-PF-UG-ULTIMA/align/ug/na/602220-20260417-2047-S16-A-Z0299-CATGCGGAGTGAGAT-prod-cram-7-CATGCGGAGTGAGAT-PF-UG-ULTIMA.ug.na.cram.crai
    wildcards: sample=602220-20260417-2047-S16-A-Z0299-CATGCGGAGTGAGAT-prod-cram-7-CATGCGGAGTGAGAT-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/602220-20260417-2047-S16-A-Z0299-CATGCGGAGTGAGAT-prod-cram-7-CATGCGGAGTGAGAT-PF-UG-ULTIMA/align/ug/na/602220-20260417-2047-S16-A-Z0299-CATGCGGAGTGAGAT-prod-cram-7-CATGCGGAGTGAGAT-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/602220-20260417-2047-S16-A-Z0299-CATGCGGAGTGAGAT-prod-cram-7-CATGCGGAGTGAGAT-PF-UG-ULTIMA/align/ug/na/alignqc/alignstats/602220-20260417-2047-S16-A-Z0299-CATGCGGAGTGAGAT-prod-cram-7-CATGCGGAGTGAGAT-PF-UG-ULTIMA.ug.na.alignstats.json  -j cram -v -P 96 -p 96 > results/day/hg38_broad/602220-20260417-2047-S16-A-Z0299-CATGCGGAGTGAGAT-prod-cram-7-CATGCGGAGTGAGAT-PF-UG-ULTIMA/align/ug/na/alignqc/alignstats/logs/602220-20260417-2047-S16-A-Z0299-CATGCGGAGTGAGAT-prod-cram-7-CATGCGGAGTGAGAT-PF-UG-ULTIMA.ug.na.alignstats.log;
Submitted job 28 with external jobid '2127'.
[Sat Apr 25 09:33:49 2026]
Finished job 61.
23 of 67 steps (34%) done
Select jobs to execute...

[Sat Apr 25 09:33:49 2026]
rule alignstats:
    input: results/day/hg38_broad/602220-20260417-2047-S6-A-Z0290-CTTGCTATGAGCGAT-prod-cram-15-CTTGCTATGAGCGAT-PF-UG-ULTIMA/align/ug/na/602220-20260417-2047-S6-A-Z0290-CTTGCTATGAGCGAT-prod-cram-15-CTTGCTATGAGCGAT-PF-UG-ULTIMA.ug.na.cram, results/day/hg38_broad/602220-20260417-2047-S6-A-Z0290-CTTGCTATGAGCGAT-prod-cram-15-CTTGCTATGAGCGAT-PF-UG-ULTIMA/align/ug/na/602220-20260417-2047-S6-A-Z0290-CTTGCTATGAGCGAT-prod-cram-15-CTTGCTATGAGCGAT-PF-UG-ULTIMA.ug.na.cram.crai
    output: results/day/hg38_broad/602220-20260417-2047-S6-A-Z0290-CTTGCTATGAGCGAT-prod-cram-15-CTTGCTATGAGCGAT-PF-UG-ULTIMA/align/ug/na/alignqc/alignstats/602220-20260417-2047-S6-A-Z0290-CTTGCTATGAGCGAT-prod-cram-15-CTTGCTATGAGCGAT-PF-UG-ULTIMA.ug.na.alignstats.json
    log: results/day/hg38_broad/602220-20260417-2047-S6-A-Z0290-CTTGCTATGAGCGAT-prod-cram-15-CTTGCTATGAGCGAT-PF-UG-ULTIMA/align/ug/na/alignqc/alignstats/logs/602220-20260417-2047-S6-A-Z0290-CTTGCTATGAGCGAT-prod-cram-15-CTTGCTATGAGCGAT-PF-UG-ULTIMA.ug.na.alignstats.log
    jobid: 60
    benchmark: results/day/hg38_broad/602220-20260417-2047-S6-A-Z0290-CTTGCTATGAGCGAT-prod-cram-15-CTTGCTATGAGCGAT-PF-UG-ULTIMA/benchmarks/602220-20260417-2047-S6-A-Z0290-CTTGCTATGAGCGAT-prod-cram-15-CTTGCTATGAGCGAT-PF-UG-ULTIMA.ug.na.alignstats.bench.tsv
    reason: Missing output files: results/day/hg38_broad/602220-20260417-2047-S6-A-Z0290-CTTGCTATGAGCGAT-prod-cram-15-CTTGCTATGAGCGAT-PF-UG-ULTIMA/align/ug/na/alignqc/alignstats/602220-20260417-2047-S6-A-Z0290-CTTGCTATGAGCGAT-prod-cram-15-CTTGCTATGAGCGAT-PF-UG-ULTIMA.ug.na.alignstats.json; Input files updated by another job: results/day/hg38_broad/602220-20260417-2047-S6-A-Z0290-CTTGCTATGAGCGAT-prod-cram-15-CTTGCTATGAGCGAT-PF-UG-ULTIMA/align/ug/na/602220-20260417-2047-S6-A-Z0290-CTTGCTATGAGCGAT-prod-cram-15-CTTGCTATGAGCGAT-PF-UG-ULTIMA.ug.na.cram.crai, results/day/hg38_broad/602220-20260417-2047-S6-A-Z0290-CTTGCTATGAGCGAT-prod-cram-15-CTTGCTATGAGCGAT-PF-UG-ULTIMA/align/ug/na/602220-20260417-2047-S6-A-Z0290-CTTGCTATGAGCGAT-prod-cram-15-CTTGCTATGAGCGAT-PF-UG-ULTIMA.ug.na.cram
    wildcards: sample=602220-20260417-2047-S6-A-Z0290-CTTGCTATGAGCGAT-prod-cram-15-CTTGCTATGAGCGAT-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/602220-20260417-2047-S6-A-Z0290-CTTGCTATGAGCGAT-prod-cram-15-CTTGCTATGAGCGAT-PF-UG-ULTIMA/align/ug/na/602220-20260417-2047-S6-A-Z0290-CTTGCTATGAGCGAT-prod-cram-15-CTTGCTATGAGCGAT-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/602220-20260417-2047-S6-A-Z0290-CTTGCTATGAGCGAT-prod-cram-15-CTTGCTATGAGCGAT-PF-UG-ULTIMA/align/ug/na/alignqc/alignstats/602220-20260417-2047-S6-A-Z0290-CTTGCTATGAGCGAT-prod-cram-15-CTTGCTATGAGCGAT-PF-UG-ULTIMA.ug.na.alignstats.json  -j cram -v -P 96 -p 96 > results/day/hg38_broad/602220-20260417-2047-S6-A-Z0290-CTTGCTATGAGCGAT-prod-cram-15-CTTGCTATGAGCGAT-PF-UG-ULTIMA/align/ug/na/alignqc/alignstats/logs/602220-20260417-2047-S6-A-Z0290-CTTGCTATGAGCGAT-prod-cram-15-CTTGCTATGAGCGAT-PF-UG-ULTIMA.ug.na.alignstats.log;
Submitted job 60 with external jobid '2128'.
[Sat Apr 25 09:34:09 2026]
Finished job 41.
24 of 67 steps (36%) done
Select jobs to execute...

[Sat Apr 25 09:34:09 2026]
rule alignstats:
    input: results/day/hg38_broad/602220-20260417-2047-S19-A-Z0300-CAGATATAGCCTGAT-prod-cram-10-CAGATATAGCCTGAT-PF-UG-ULTIMA/align/ug/na/602220-20260417-2047-S19-A-Z0300-CAGATATAGCCTGAT-prod-cram-10-CAGATATAGCCTGAT-PF-UG-ULTIMA.ug.na.cram, results/day/hg38_broad/602220-20260417-2047-S19-A-Z0300-CAGATATAGCCTGAT-prod-cram-10-CAGATATAGCCTGAT-PF-UG-ULTIMA/align/ug/na/602220-20260417-2047-S19-A-Z0300-CAGATATAGCCTGAT-prod-cram-10-CAGATATAGCCTGAT-PF-UG-ULTIMA.ug.na.cram.crai
    output: results/day/hg38_broad/602220-20260417-2047-S19-A-Z0300-CAGATATAGCCTGAT-prod-cram-10-CAGATATAGCCTGAT-PF-UG-ULTIMA/align/ug/na/alignqc/alignstats/602220-20260417-2047-S19-A-Z0300-CAGATATAGCCTGAT-prod-cram-10-CAGATATAGCCTGAT-PF-UG-ULTIMA.ug.na.alignstats.json
    log: results/day/hg38_broad/602220-20260417-2047-S19-A-Z0300-CAGATATAGCCTGAT-prod-cram-10-CAGATATAGCCTGAT-PF-UG-ULTIMA/align/ug/na/alignqc/alignstats/logs/602220-20260417-2047-S19-A-Z0300-CAGATATAGCCTGAT-prod-cram-10-CAGATATAGCCTGAT-PF-UG-ULTIMA.ug.na.alignstats.log
    jobid: 40
    benchmark: results/day/hg38_broad/602220-20260417-2047-S19-A-Z0300-CAGATATAGCCTGAT-prod-cram-10-CAGATATAGCCTGAT-PF-UG-ULTIMA/benchmarks/602220-20260417-2047-S19-A-Z0300-CAGATATAGCCTGAT-prod-cram-10-CAGATATAGCCTGAT-PF-UG-ULTIMA.ug.na.alignstats.bench.tsv
    reason: Missing output files: results/day/hg38_broad/602220-20260417-2047-S19-A-Z0300-CAGATATAGCCTGAT-prod-cram-10-CAGATATAGCCTGAT-PF-UG-ULTIMA/align/ug/na/alignqc/alignstats/602220-20260417-2047-S19-A-Z0300-CAGATATAGCCTGAT-prod-cram-10-CAGATATAGCCTGAT-PF-UG-ULTIMA.ug.na.alignstats.json; Input files updated by another job: results/day/hg38_broad/602220-20260417-2047-S19-A-Z0300-CAGATATAGCCTGAT-prod-cram-10-CAGATATAGCCTGAT-PF-UG-ULTIMA/align/ug/na/602220-20260417-2047-S19-A-Z0300-CAGATATAGCCTGAT-prod-cram-10-CAGATATAGCCTGAT-PF-UG-ULTIMA.ug.na.cram, results/day/hg38_broad/602220-20260417-2047-S19-A-Z0300-CAGATATAGCCTGAT-prod-cram-10-CAGATATAGCCTGAT-PF-UG-ULTIMA/align/ug/na/602220-20260417-2047-S19-A-Z0300-CAGATATAGCCTGAT-prod-cram-10-CAGATATAGCCTGAT-PF-UG-ULTIMA.ug.na.cram.crai
    wildcards: sample=602220-20260417-2047-S19-A-Z0300-CAGATATAGCCTGAT-prod-cram-10-CAGATATAGCCTGAT-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/602220-20260417-2047-S19-A-Z0300-CAGATATAGCCTGAT-prod-cram-10-CAGATATAGCCTGAT-PF-UG-ULTIMA/align/ug/na/602220-20260417-2047-S19-A-Z0300-CAGATATAGCCTGAT-prod-cram-10-CAGATATAGCCTGAT-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/602220-20260417-2047-S19-A-Z0300-CAGATATAGCCTGAT-prod-cram-10-CAGATATAGCCTGAT-PF-UG-ULTIMA/align/ug/na/alignq--output truncated--
