** AUGMENT CODE RULE ** MUST NOT DO : DO NOT USE heredoc. heredoc always corrupts termainals.
** AUGMENT CODE RULE ** MUST DO : YOU MUST use tmp script to run all commands innstead of redirecting strings printed to terminal (ie: heredoc), if you do anything other than use scripts, terminals get corrupted.
BASH=/bin/bash
BASH_ARGC=([0]="1")
BASH_ARGV=([0]="pipefail")
BASH_EXECUTION_STRING=set
BASH_LINENO=()
BASH_SOURCE=()
BASH_VERSINFO=([0]="3" [1]="2" [2]="57" [3]="1" [4]="release" [5]="arm64-apple-darwin25")
BASH_VERSION='3.2.57(1)-release'
CODEX_CI=1
CODEX_INTERNAL_ORIGINATOR_OVERRIDE='Codex Desktop'
CODEX_SHELL=1
CODEX_THREAD_ID=019e9015-6e7f-7e43-8486-49046a17534b
COLORTERM=
COMMAND_MODE=unix2003
CONDA_DEFAULT_ENV=base
CONDA_EXE=/Users/jmajor/miniconda3/bin/conda
CONDA_PREFIX=/Users/jmajor/miniconda3
CONDA_PROMPT_MODIFIER='(base) '
CONDA_PYTHON_EXE=/Users/jmajor/miniconda3/bin/python
CONDA_SHLVL=1
DIRSTACK=()
DISABLE_AUTO_UPDATE=true
EUID=501
GH_PAGER=cat
GIT_PAGER=cat
GROUPS=()
HOME=/Users/jmajor
HOSTNAME=Johns-MacBook-Pro.local
HOSTTYPE=arm64
IFS=$' \t\n'
LANG=C.UTF-8
LC_ALL=C.UTF-8
LC_CTYPE=C.UTF-8
LOGNAME=jmajor
LOG_FORMAT=json
MACHTYPE=arm64-apple-darwin25
MallocNanoZone=0
NO_COLOR=1
OPTERR=1
OPTIND=1
OSLogRateLimit=64
OSTYPE=darwin25
PAGER=cat
PATH=/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/pkg/env/global/bin:/Library/Apple/usr/bin:/opt/homebrew/bin:/Users/jmajor/.codex/tmp/arg0/codex-arg0wVr1rQ:/Users/jmajor/miniconda3/bin:/Users/jmajor/miniconda3/condabin:/Applications/Codex.app/Contents/Resources
PIPESTATUS=([0]="0")
PPID=14993
PS1='(base) '
PS4='+ '
PWD=/Users/jmajor/projects/lsmc/daylily-ephemeral-cluster
RUST_LOG=warn
SHELL=/bin/zsh
SHELLOPTS=braceexpand:hashall:interactive-comments
SHLVL=3
SSH_AUTH_SOCK=/var/run/com.apple.launchd.n46yQXkmau/Listeners
TERM=dumb
TMPDIR=/var/folders/rk/2n95m40s1zs48qr48ynwhxwm0000gn/T/
UID=501
USER=jmajor
XPC_FLAGS=0x0
XPC_SERVICE_NAME=0
ZSH_TMUX_AUTOSTART=false
ZSH_TMUX_AUTOSTARTED=true
_='** AUGMENT CODE RULE ** MUST DO : YOU MUST use tmp script to run all commands innstead of redirecting strings printed to terminal (ie: heredoc), if you do anything other than use scripts, terminals get corrupted.'
_CE_CONDA=
_CE_M=
_CONDA_EXE=/Users/jmajor/miniconda3/bin/conda
_CONDA_ROOT=/Users/jmajor/miniconda3
__CFBundleIdentifier=com.openai.codex
__CF_USER_TEXT_ENCODING=0x1F5:0x0:0x0
__conda_activate () 
{ 
    if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
        PS1="$CONDA_PS1_BACKUP";
        \unset CONDA_PS1_BACKUP;
    fi;
    \local ask_conda;
    ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return;
    \eval "$ask_conda";
    __conda_hashr
}
__conda_exe () 
{ 
    ( if [ -n "${_CE_M:+x}" ] && [ -n "${_CE_CONDA:+x}" ]; then
        "$CONDA_EXE" $_CE_M $_CE_CONDA "$@";
    else
        "$CONDA_EXE" "$@";
    fi )
}
__conda_hashr () 
{ 
    if [ -n "${ZSH_VERSION:+x}" ]; then
        \rehash;
    else
        if [ -n "${POSH_VERSION:+x}" ]; then
            :;
        else
            \hash -r;
        fi;
    fi
}
__conda_reactivate () 
{ 
    echo "'__conda_reactivate' is deprecated and will be removed in 25.9. Use '__conda_activate reactivate' instead." 1>&2;
    __conda_activate reactivate
}
conda () 
{ 
    \local cmd="${1-__missing__}";
    case "$cmd" in 
        activate | deactivate)
            __conda_activate "$@"
        ;;
        install | update | upgrade | remove | uninstall)
            __conda_exe "$@" || \return;
            __conda_activate reactivate
        ;;
        *)
            __conda_exe "$@"
        ;;
    esac
}
required
2026-06-06 03:15:30   12675488 DAY_final_multiqc.html
2026-06-06 03:15:30   26705126 multiqc_data.json
2026-06-06 03:15:30    4177078 dayoa_evidence_manifest.json
summary
2026-06-06 03:15:30      13734 derived/analysis_results/hyb-only/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/workflow/scripts/parse_bclconvert_samplesheet.py
2026-06-06 03:15:29       5962 derived/analysis_results/hyb-only/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/workflow/scripts/parse_truvari_summary.py
2026-06-06 03:15:30       5624 derived/analysis_results/hyb-only/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/workflow/scripts/prepare_bclconvert_demux_fastqc_inputs.py
2026-06-06 03:15:30       6615 derived/analysis_results/hyb-only/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/workflow/scripts/prepare_bclconvert_lane_samplesheet.py
2026-06-06 03:15:29      11744 derived/analysis_results/hyb-only/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/workflow/scripts/relatedness_report.py
2026-06-06 03:15:30       9119 derived/analysis_results/hyb-only/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/workflow/scripts/run_bclconvert_lane.sh
2026-06-06 03:15:30        717 derived/analysis_results/hyb-only/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/workflow/scripts/sort_concat_chrm_list.py
2026-06-06 03:15:30      30718 derived/analysis_results/hyb-only/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/workflow/scripts/stage_multiqc_inputs.py
2026-06-06 03:15:29       6647 derived/analysis_results/hyb-only/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/workflow/scripts/summarize_run_qc_report.py
2026-06-06 03:15:29       7350 derived/analysis_results/hyb-only/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/workflow/scripts/summarize_unmapped_ganon2.py
2026-06-06 03:15:29       7141 derived/analysis_results/hyb-only/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/workflow/scripts/summarize_unmapped_metagenomics.py
2026-06-06 03:15:30       9606 derived/analysis_results/hyb-only/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/workflow/scripts/summarize_unmapped_sourmash.py
2026-06-06 03:15:29       3656 derived/analysis_results/hyb-only/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/workflow/scripts/tiddit_sv_to_multiqc.py
2026-06-06 03:15:29       3810 derived/analysis_results/hyb-only/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/workflow/scripts/validate_multiqc_sample_ids.py
2026-06-06 03:15:30        138 derived/analysis_results/hyb-only/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/workflow/scripts/write_dayoa_evidence_manifest.py
2026-06-06 03:15:30       2937 derived/analysis_results/hyb-only/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/workflow/scripts/write_illumina_run_qc_json.py
2026-06-06 03:15:29       2417 derived/analysis_results/hyb-only/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/workflow/scripts/write_interop_summary_csv.py

Total Objects: 16042
   Total Size: 255917543393
