DAY-EC activated.
DAY-EC activated.
time=2026-05-30T16:25:02Z
squeue:
processes:
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1871708       1 S          06:13  0.0  0.0 sleep 900
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1874376       1 S          01:15  0.0  0.0 sleep 900
1874933 1874932 S          00:04  0.2  0.0 bash -l /tmp/daylily-ssm-OGeyDF.sh
1875034 1874933 R          00:00  0.0  0.0 ps -u ubuntu -o pid,ppid,stat,etime,pcpu,pmem,cmd --sort=start_time
1875035 1874933 S          00:00  0.0  0.0 tail -80
direct status:
{
  "command": "bin/day_run produce_bclconvert_fastqs_and_metrics -p -j 20 -k --config run_context_file=config/runs.tsv bootstrap_bclconvert=true",
  "completed_at": "2026-05-30T16:23:49Z",
  "exit_code": 1,
  "repo_path": "/fsx/analysis_results/ubuntu/ccv20260530r42_illumina_bclconvert/daylily-omics-analysis",
  "session_name": "ccv20260530r42_bclconvert_rc0_direct",
  "started_at": "2026-05-30T16:23:36Z"
}

latest snakemake log:
WorkflowError in file /fsx/analysis_results/ubuntu/ccv20260530r42_illumina_bclconvert/daylily-omics-analysis/workflow/rules/common.smk, line 1533:


MANIFEST ERROR 20260514_LH01106_0009_B23TVLGLT4-HG001-a-GAGTAATATA.TCACGGTCGG.1-1-GAGTAATATACCGACCGTGA-PCR-FREE-ILMN-NOVASEQ ... 20260514_LH01106_0009_B23TVLGLT4-HG001-a-GAGTAATATA.TCACGGTCGG.1-1-GAGTAATATACCGACCGTGA-PCR-FREE-ILMN-NOVASEQ: SQ/RU/EX/LANE may not contain '.' or '_' per current constraints.
  File "/fsx/analysis_results/ubuntu/ccv20260530r42_illumina_bclconvert/daylily-omics-analysis/workflow/Snakefile", line 66, in <module>
  File "/fsx/analysis_results/ubuntu/ccv20260530r42_illumina_bclconvert/daylily-omics-analysis/workflow/rules/global_common.smk", line 151, in <module>
  File "/fsx/analysis_results/ubuntu/ccv20260530r42_illumina_bclconvert/daylily-omics-analysis/workflow/rules/common.smk", line 1533, in <module>
