Completed 27 Bytes/27 Bytes (160 Bytes/s) with 1 file(s) remaining
upload: ../../../../../../var/folders/rk/2n95m40s1zs48qr48ynwhxwm0000gn/T/tmpz0d9z18i to s3://lsmc-ssf-sequencing-data/staged_external_data/remote_stage_20260529T202437Z_6ac53e3a/_write_test.txt
delete: s3://lsmc-ssf-sequencing-data/staged_external_data/remote_stage_20260529T202437Z_6ac53e3a/_write_test.txt
Completed 8.0 MiB/77.6 MiB (15.4 MiB/s) with 1 file(s) remaining
Completed 16.0 MiB/77.6 MiB (30.2 MiB/s) with 1 file(s) remaining
Completed 24.0 MiB/77.6 MiB (44.1 MiB/s) with 1 file(s) remaining
Completed 32.0 MiB/77.6 MiB (58.5 MiB/s) with 1 file(s) remaining
Completed 40.0 MiB/77.6 MiB (69.9 MiB/s) with 1 file(s) remaining
Completed 48.0 MiB/77.6 MiB (82.0 MiB/s) with 1 file(s) remaining
Completed 56.0 MiB/77.6 MiB (90.9 MiB/s) with 1 file(s) remaining
Completed 64.0 MiB/77.6 MiB (102.8 MiB/s) with 1 file(s) remaining
Completed 72.0 MiB/77.6 MiB (110.5 MiB/s) with 1 file(s) remaining
Completed 77.6 MiB/77.6 MiB (114.9 MiB/s) with 1 file(s) remaining
copy: s3://lsmc-dayoa-control-data-usw2/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/downsampled/HG002_0.1x_R1.fastq.gz to s3://lsmc-ssf-sequencing-data/staged_external_data/remote_stage_20260529T202437Z_6ac53e3a/JEMILMN0P1_HG002-NOVASEQ-PF-gdna-0p1x_D0_0/HG002_0.1x_R1.fastq.gz
Completed 8.0 MiB/79.5 MiB (14.2 MiB/s) with 1 file(s) remaining
Completed 16.0 MiB/79.5 MiB (28.4 MiB/s) with 1 file(s) remaining
Completed 24.0 MiB/79.5 MiB (42.1 MiB/s) with 1 file(s) remaining
Completed 32.0 MiB/79.5 MiB (55.9 MiB/s) with 1 file(s) remaining
Completed 40.0 MiB/79.5 MiB (68.8 MiB/s) with 1 file(s) remaining
Completed 48.0 MiB/79.5 MiB (80.0 MiB/s) with 1 file(s) remaining
Completed 56.0 MiB/79.5 MiB (91.7 MiB/s) with 1 file(s) remaining
Completed 64.0 MiB/79.5 MiB (101.8 MiB/s) with 1 file(s) remaining
Completed 71.5 MiB/79.5 MiB (110.1 MiB/s) with 1 file(s) remaining
Completed 79.5 MiB/79.5 MiB (120.1 MiB/s) with 1 file(s) remaining
copy: s3://lsmc-dayoa-control-data-usw2/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/downsampled/HG002_0.1x_R2.fastq.gz to s3://lsmc-ssf-sequencing-data/staged_external_data/remote_stage_20260529T202437Z_6ac53e3a/JEMILMN0P1_HG002-NOVASEQ-PF-gdna-0p1x_D0_0/HG002_0.1x_R2.fastq.gz
Completed 442 Bytes/442 Bytes (2.5 KiB/s) with 1 file(s) remaining
upload: docs/plans/20260526T223700Z_goodole3_inputs/20260529T202437Z_6ac53e3a_samples.tsv to s3://lsmc-ssf-sequencing-data/staged_external_data/remote_stage_20260529T202437Z_6ac53e3a/20260529T202437Z_6ac53e3a_samples.tsv
Completed 976 Bytes/976 Bytes (5.5 KiB/s) with 1 file(s) remaining
upload: docs/plans/20260526T223700Z_goodole3_inputs/20260529T202437Z_6ac53e3a_units.tsv to s3://lsmc-ssf-sequencing-data/staged_external_data/remote_stage_20260529T202437Z_6ac53e3a/20260529T202437Z_6ac53e3a_units.tsv
Precheck passed: rows checked=1, samples checked=1, source objects checked=32, concordance directories checked=1.
Remote staging completed successfully.
Remote FSx stage directory: /fsx/staging/staged_external_sequencing_data/remote_stage_20260529T202437Z_6ac53e3a
Staging DRA: dra-08f17ef718d845a1e
Staging DRA lifecycle: AVAILABLE
Staged files (2):
  /fsx/staging/staged_external_sequencing_data/remote_stage_20260529T202437Z_6ac53e3a/JEMILMN0P1_HG002-NOVASEQ-PF-gdna-0p1x_D0_0/HG002_0.1x_R1.fastq.gz
  /fsx/staging/staged_external_sequencing_data/remote_stage_20260529T202437Z_6ac53e3a/JEMILMN0P1_HG002-NOVASEQ-PF-gdna-0p1x_D0_0/HG002_0.1x_R2.fastq.gz
Generated configuration files:
  samples.tsv -> s3://lsmc-ssf-sequencing-data/staged_external_data/remote_stage_20260529T202437Z_6ac53e3a/20260529T202437Z_6ac53e3a_samples.tsv
  units.tsv   -> s3://lsmc-ssf-sequencing-data/staged_external_data/remote_stage_20260529T202437Z_6ac53e3a/20260529T202437Z_6ac53e3a_units.tsv
DAY-EC activated.
DAY-EC activated.
__DAYLILY_STAGE_DIR__=/fsx/staging/staged_external_sequencing_data/remote_stage_20260529T202437Z_6ac53e3a
__DAYLILY_STAGE_SAMPLES__=/fsx/staging/staged_external_sequencing_data/remote_stage_20260529T202437Z_6ac53e3a/20260529T202437Z_6ac53e3a_samples.tsv
__DAYLILY_STAGE_UNITS__=/fsx/staging/staged_external_sequencing_data/remote_stage_20260529T202437Z_6ac53e3a/20260529T202437Z_6ac53e3a_units.tsv
DAY-EC activated.
DAY-EC activated.
__DAYLILY_SESSION__=ccv20260529r5_illumina_hg002_kitchensink_multiqc_dryrun
__DAYLILY_RUN_DIR__=/home/ubuntu/daylily-runs/ccv20260529r5_illumina_hg002_kitchensink_multiqc_dryrun
__DAYLILY_REPO_PATH__=/fsx/analysis_results/ubuntu/ccv20260529r5_illumina_hg002_kitchensink_multiqc_dryrun/daylily-omics-analysis
Tmux session 'ccv20260529r5_illumina_hg002_kitchensink_multiqc_dryrun' created on the head node.
Run state directory: /home/ubuntu/daylily-runs/ccv20260529r5_illumina_hg002_kitchensink_multiqc_dryrun
Workflow repo path: /fsx/analysis_results/ubuntu/ccv20260529r5_illumina_hg002_kitchensink_multiqc_dryrun/daylily-omics-analysis
Reconnect with: daylily-ssh-into-headnode --profile lsmc --region us-west-2 --cluster dyec-test
Then run: tmux attach -t ccv20260529r5_illumina_hg002_kitchensink_multiqc_dryrun
Samples run receipt: /Users/jmajor/.codex/worktrees/dyec-fsx-dra-mounts/daylily-ephemeral-cluster/docs/plans/20260526T223700Z_goodole3_inputs/20260529T202437Z_6ac53e3a_samples_run_receipt.json
