DAY-EC activated.
DAY-EC activated.
=== markers ===
196:Building DAG of jobs...
198:Job stats:
233:    reason: Missing output files: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.R2.fastq.gz, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.R1.fastq.gz
244:    reason: Missing output files: logs/supporting_data_staging.done
255:    reason: Missing output files: logs/workflow_staging.done; Input files updated by another job: logs/supporting_data_staging.done
262:Reason: Missing output files: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.dirsetup.ready; Input files updated by another job: logs/workflow_staging.done
265:        ( mkdir -p $(dirname results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.dirsetup.ready ) || echo "ERROR:: mkdir $(dirname results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.dirsetup.ready )  FAILED";
276:    reason: Missing output files: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.sort.bam.bai, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.sort.bam; Input files updated by another job: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.R2.fastq.gz, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.R1.fastq.gz, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.dirsetup.ready
301:        ulimit -n 65536 || echo "ulimit mod failed" > results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/logs/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.sort.log 2>&1;
363:    reason: Missing output files: results/day/hg38_broad/logs/target_aliases/produce_sentcg_align.done; Input files updated by another job: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.sort.bam
375:    reason: Missing output files: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cram, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cram.crai; Input files updated by another job: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.sort.bam.bai, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.sort.bam
390:        ulimit -n 65536 || echo "ulimit mod failed" > results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/logs/dedupe.dmd.TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.log 2>&1;
417:    reason: Missing output files: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/na/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.na.cram.crai, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/na/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.na.cram; Input files updated by another job: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.sort.bam.bai, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.sort.bam
441:Would remove temporary output results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.sort.bam.bai
442:Would remove temporary output results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.sort.bam
450:    reason: Missing output files: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/vcfs/1-24/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.ready; Input files updated by another job: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cram, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cram.crai
466:    reason: Missing output files: results/day/hg38_broad/logs/target_aliases/produce_dmd_dedup_cram.done; Input files updated by another job: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cram
478:    reason: Missing output files: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/na/alignqc/alignstats/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.na.alignstats.json; Input files updated by another job: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/na/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.na.cram.crai, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/na/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.na.cram
492:    reason: Missing output files: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/alignqc/alignstats/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.alignstats.json; Input files updated by another job: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cram, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cram.crai
504:    reason: Missing output files: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/alignqc/alignstats/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.alignstats.tsv; Input files updated by another job: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/alignqc/alignstats/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.alignstats.json
514:    reason: Missing output files: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/na/alignqc/alignstats/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.na.alignstats.tsv; Input files updated by another job: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/na/alignqc/alignstats/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.na.alignstats.json
526:    reason: Missing output files: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/vcfs/1-24/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.vcf; Input files updated by another job: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cram, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/vcfs/1-24/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.ready, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cram.crai
545:        ulimit -n 65536 || echo "ulimit mod failed" > results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/log/vcfs/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.log 2>&1;
574:Would remove temporary output results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/vcfs/1-24/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.vcf.tmp
583:    reason: Missing output files: results/day/hg38_broad/other_reports/alignstats_summary_gather.done; Input files updated by another job: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/alignqc/alignstats/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.alignstats.tsv, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/na/alignqc/alignstats/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.na.alignstats.tsv
594:    reason: Missing output files: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/vcfs/1-24/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.sort.vcf.gz.tbi; Input files updated by another job: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/vcfs/1-24/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.vcf
604:Would remove temporary output results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/vcfs/1-24/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.vcf
605:Would remove temporary output results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/vcfs/1-24/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.sort.vcf
614:    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
630:    reason: Missing output files: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.concat.vcf.gz.fofn; Input files updated by another job: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/vcfs/1-24/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.sort.vcf.gz.tbi
643:Would remove temporary output results/day/hg38_broad/other_reports/alignstats_csummary.tsv
659:    reason: Missing output files: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.sort.vcf.gz, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.sort.vcf.gz.tbi; Input files updated by another job: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.concat.vcf.gz.fofn
678:Would remove temporary output results/day/hg38_broad/other_reports/alignstats_bsummary.tsv
679:Would remove temporary output results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.sort.temp.vcf.gz
686:    reason: Missing output files: results/day/hg38_broad/logs/target_aliases/produce_cgt7p_snv_vcf.done; Input files updated by another job: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.sort.vcf.gz.tbi
698:    reason: Missing output files: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_hg38/summary.txt; Input files updated by another job: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.sort.vcf.gz, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.sort.vcf.gz.tbi
703:RuleException in rule rtg_vcfeval_roi in file /fsx/analysis_results/ubuntu/ccv20260530r53_complete_genomics_mgi_snv_concordance_dryrun/daylily-omics-analysis/workflow/rules/rtg_vcfeval.smk, line 167:
704:NameError: The name 'rtg_mem_gb' is unknown in this context. Please make sure that you defined that variable. Also note that braces not used for variable access have to be escaped by repeating them, i.e. {{print $1}}, when formatting the following:
=== last line count and selected tail line numbers ===
726 /home/ubuntu/daylily-runs/ccv20260530r53_complete_genomics_mgi_snv_concordance_dryrun/tmux.log

    threads: 16

              -t {params.sdf} \
              --threads {threads} \
              > {log} 2>&1

[5m[48;5;118m[30mRETURN CODE: 1[0m
[INFO] Workflow exited with status 1
DAY-EC activated.
