!=0
'#'=1
'$'=85693
'*'=( pipefail )
-=569Xl
0=-euo
'?'=0
@=( pipefail )
ARGC=1
CDPATH=''
CODEX_CI=1
CODEX_INTERNAL_ORIGINATOR_OVERRIDE='Codex Desktop'
CODEX_SHELL=1
CODEX_THREAD_ID=019e9015-6e7f-7e43-8486-49046a17534b
COLORTERM=''
COLUMNS=0
COMMAND_MODE=unix2003
CONDA_DEFAULT_ENV=base
CONDA_EXE=/Users/jmajor/miniconda3/bin/conda
CONDA_PREFIX=/Users/jmajor/miniconda3
CONDA_PROMPT_MODIFIER='(base)'
CONDA_PYTHON_EXE=/Users/jmajor/miniconda3/bin/python
CONDA_SHLVL=1
CPUTYPE=arm64
DISABLE_AUTO_UPDATE=true
EGID=20
EUID=501
FIGNORE=''
FPATH=/usr/local/share/zsh/site-functions:/usr/share/zsh/site-functions:/usr/share/zsh/5.9/functions
FUNCNEST=700
GH_PAGER=cat
GID=20
GIT_PAGER=cat
HISTCHARS='!^#'
HISTCMD=0
HISTSIZE=30
HOME=/Users/jmajor
HOST=Johns-MacBook-Pro.local
IFS=$' \t\n\C-@'
KEYBOARD_HACK=''
KEYTIMEOUT=40
LANG=C.UTF-8
LC_ALL=C.UTF-8
LC_CTYPE=C.UTF-8
LINENO=1
LINES=0
LISTMAX=100
LOGNAME=jmajor
LOG_FORMAT=json
MACHTYPE=x86_64
MAILCHECK=60
MAILPATH=''
MANPATH=''
MODULE_PATH=/usr/lib/zsh/5.9
MallocNanoZone=0
NO_COLOR=1
NULLCMD=cat
OLDPWD=/Users/jmajor/projects/lsmc/daylily-ephemeral-cluster
OPTARG=''
OPTIND=1
OSLogRateLimit=64
OSTYPE=darwin25.0
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
PPID=85606
PROMPT=''
PROMPT2=''
PROMPT3='?# '
PROMPT4='+%N:%i> '
PS1=''
PS2=''
PS3='?# '
PS4='+%N:%i> '
PSVAR=''
PWD=/Users/jmajor/projects/lsmc/daylily-ephemeral-cluster
RANDOM=23091
READNULLCMD=more
RUST_LOG=warn
SAVEHIST=0
SECONDS=0
SHELL=/bin/zsh
SHLVL=3
SPROMPT='zsh: correct '\''%R'\'' to '\''%r'\'' [nyae]? '
SSH_AUTH_SOCK=/var/run/com.apple.launchd.n46yQXkmau/Listeners
TERM=dumb
TIMEFMT='%J  %U user %S system %P cpu %*E total'
TMPDIR=/var/folders/rk/2n95m40s1zs48qr48ynwhxwm0000gn/T/
TMPPREFIX=/tmp/zsh
TRY_BLOCK_ERROR=-1
TRY_BLOCK_INTERRUPT=-1
TTY=''
TTYIDLE=-1
UID=501
USER=jmajor
USERNAME=jmajor
VENDOR=apple
WATCH
WORDCHARS='*?_-.[]~=/&;!#$%^(){}<>'
XPC_FLAGS=0x0
XPC_SERVICE_NAME=0
ZSH_ARGZERO=-euo
ZSH_EVAL_CONTEXT=cmdarg
ZSH_EXECUTION_STRING=set
ZSH_NAME=zsh
ZSH_PATCHLEVEL=zsh-5.9-0-g73d3173
ZSH_SUBSHELL=0
ZSH_TMUX_AUTOSTART=false
ZSH_TMUX_AUTOSTARTED=true
ZSH_VERSION=5.9
_=set
_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
aliases
argv=( pipefail )
builtins
cdpath=(  )
commands
dirstack
dis_aliases
dis_builtins
dis_functions
dis_functions_source
dis_galiases
dis_patchars
dis_reswords
dis_saliases
fignore=(  )
fpath=( /usr/local/share/zsh/site-functions /usr/share/zsh/site-functions /usr/share/zsh/5.9/functions )
funcfiletrace
funcsourcetrace
funcstack
functions
functions_source
functrace
galiases
histchars='!^#'
history
historywords
jobdirs
jobstates
jobtexts
keymaps
mailpath=(  )
manpath=(  )
module_path=( /usr/lib/zsh/5.9 )
modules
nameddirs
options
parameters
patchars
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 )
prompt=''
psvar=(  )
reswords
saliases
signals=( EXIT HUP INT QUIT ILL TRAP ABRT EMT FPE KILL BUS SEGV SYS PIPE ALRM TERM URG STOP TSTP CONT CHLD TTIN TTOU IO XCPU XFSZ VTALRM PROF WINCH INFO USR1 USR2 ZERR DEBUG )
status=0
termcap
terminfo
userdirs
usergroups
watch
widgets
zsh_eval_context=( cmdarg )
zsh_scheduled_events
{
  "command": "bin/day_run produce_sent_align produce_dmd_dedup_cram produce_sentdhiomr_snv_vcf produce_sentdhiomr_sv produce_sentdhiomr_cnv produce_sentdhiomr_segdup produce_sentdhiomr_mito produce_expansionhunter produce_alignstats --config 'aligners=[\"sent\"]' 'dedupers=[\"dmd\"]' 'snv_callers=[\"sentdhiomr\"]' 'sv_callers=[\"sentdhiomr\"]' 'sentdhiomr={\"segdup_genes\":\"CYP11B1,NCF1,SMN1\"}' -j 125 -p -k --rerun-triggers mtime -n",
  "completed_at": "2026-06-06T12:31:16Z",
  "exit_code": 0,
  "repo_path": "/fsx/analysis_results/ubuntu/hybonly_hybrid_hiomr_na2_chip12_varalign_dryrun_20260606T122800Z/daylily-omics-analysis",
  "session_name": "hybonly_hybrid_hiomr_na2_chip12_varalign_dryrun_20260606T122800Z",
  "started_at": "2026-06-06T12:30:50Z"
}

## LOGS
DAY-EC activated.
DAY-EC activated.
        set -euo pipefail
        export PATH=$PATH:/fsx/references/runtime_assets/cached_envs/sentieon-genomics-202503.02/bin/

        echo "Starting final normalization at $(date)" >> results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.16.final_norm.log

        bcftools view --threads 8 -a -e 'GT="0/0"' results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/16/tmp/combined_apply.vcf.gz 2>> results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.16.final_norm.log |         bcftools norm --threads 8 -f /fsx/references/genomic_data/organism_references/H_sapiens/hg38_broad/Homo_sapiens_assembly38.fasta 2>> results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.16.final_norm.log |         bin/dayoa_sentieon util vcfconvert -t 8 - results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/16/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.16.snv.sort.vcf.gz >> results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.16.final_norm.log 2>&1

        echo "Final normalization completed at $(date)" >> results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.16.final_norm.log
        

[Sat Jun  6 12:31:15 2026]
rule sentdhiomr_final_norm:
    input: results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/2/tmp/combined_apply.vcf.gz
    output: results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/2/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.2.snv.sort.vcf.gz, results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/2/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.2.snv.sort.vcf.gz.tbi
    log: results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.2.final_norm.log
    jobid: 56
    benchmark: results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ/benchmarks/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.2.final_norm.bench.tsv
    reason: Missing output files: results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/2/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.2.snv.sort.vcf.gz.tbi; Input files updated by another job: results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/2/tmp/combined_apply.vcf.gz
    wildcards: sample=HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ, alnr=ont, ddup=dmd, dchrm=2
    threads: 8
    resources: mem_mb=16000, mem_mib=15259, disk_mb=1000, disk_mib=954, tmpdir=<TBD>, threads=8, time=5440, partition=i192mem,i192bigmem, vcpu=8, distribution=block, exclusive=, constraint=, exclude=, include=


        set -euo pipefail
        export PATH=$PATH:/fsx/references/runtime_assets/cached_envs/sentieon-genomics-202503.02/bin/

        echo "Starting final normalization at $(date)" >> results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.2.final_norm.log

        bcftools view --threads 8 -a -e 'GT="0/0"' results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/2/tmp/combined_apply.vcf.gz 2>> results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.2.final_norm.log |         bcftools norm --threads 8 -f /fsx/references/genomic_data/organism_references/H_sapiens/hg38_broad/Homo_sapiens_assembly38.fasta 2>> results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.2.final_norm.log |         bin/dayoa_sentieon util vcfconvert -t 8 - results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/2/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.2.snv.sort.vcf.gz >> results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.2.final_norm.log 2>&1

        echo "Final normalization completed at $(date)" >> results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.2.final_norm.log
        

[Sat Jun  6 12:31:15 2026]
localrule sentdhiomr_concat_fofn:
    input: results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/1/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.1.snv.sort.vcf.gz.tbi, results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/2/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.2.snv.sort.vcf.gz.tbi, results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/3/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.3.snv.sort.vcf.gz.tbi, results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/4/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.4.snv.sort.vcf.gz.tbi, results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/5/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.5.snv.sort.vcf.gz.tbi, results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/6/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.6.snv.sort.vcf.gz.tbi, results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/7/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.7.snv.sort.vcf.gz.tbi, results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/8/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.8.snv.sort.vcf.gz.tbi, results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/9/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.9.snv.sort.vcf.gz.tbi, results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/10/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.10.snv.sort.vcf.gz.tbi, results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/11/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.11.snv.sort.vcf.gz.tbi, results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/12/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.12.snv.sort.vcf.gz.tbi, results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/13/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.13.snv.sort.vcf.gz.tbi, results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/14/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.14.snv.sort.vcf.gz.tbi, results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/15/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.15.snv.sort.vcf.gz.tbi, results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/16/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.16.snv.sort.vcf.gz.tbi, results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/17-19/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.17-19.snv.sort.vcf.gz.tbi, results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/20-25/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.20-25.snv.sort.vcf.gz.tbi
    output: results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.concat.vcf.gz.fofn, results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.concat.vcf.gz.fofn.tmp
    log: results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.concat.fofn.log
    jobid: 737
    benchmark: results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/benchmarks/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.concat.fofn.bench.tsv
    reason: Missing output files: results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.concat.vcf.gz.fofn; Input files updated by another job: results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/15/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.15.snv.sort.vcf.gz.tbi, results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/8/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.8.snv.sort.vcf.gz.tbi, results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/11/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.11.snv.sort.vcf.gz.tbi, results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/13/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.13.snv.sort.vcf.gz.tbi, results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/17-19/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.17-19.snv.sort.vcf.gz.tbi, results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/14/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.14.snv.sort.vcf.gz.tbi, results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/10/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.10.snv.sort.vcf.gz.tbi, results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/12/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.12.snv.sort.vcf.gz.tbi, results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/3/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.3.snv.sort.vcf.gz.tbi, results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/6/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.6.snv.sort.vcf.gz.tbi, results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/7/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.7.snv.sort.vcf.gz.tbi, results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/16/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.16.snv.sort.vcf.gz.tbi, results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/20-25/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.20-25.snv.sort.vcf.gz.tbi, results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/5/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.5.snv.sort.vcf.gz.tbi, results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/1/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.1.snv.sort.vcf.gz.tbi, results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/9/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.9.snv.sort.vcf.gz.tbi, results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/2/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.2.snv.sort.vcf.gz.tbi, results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/4/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.4.snv.sort.vcf.gz.tbi
    wildcards: sample=HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ, alnr=ont, ddup=dmd
    priority: 44
    resources: mem_mb=3000, mem_mib=2862, disk_mb=1000, disk_mib=954, tmpdir=/dev/shm, threads=1, time=5440, partition=i192,i128,i192mem,bcl2fq-i384-nvme-test, vcpu=1, distribution=block, exclusive=, constraint=, exclude=, include=


        for i in results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/1/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.1.snv.sort.vcf.gz.tbi results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/2/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.2.snv.sort.vcf.gz.tbi results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/3/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.3.snv.sort.vcf.gz.tbi results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/4/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.4.snv.sort.vcf.gz.tbi results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/5/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.5.snv.sort.vcf.gz.tbi results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/6/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.6.snv.sort.vcf.gz.tbi results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/7/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.7.snv.sort.vcf.gz.tbi results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/8/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.8.snv.sort.vcf.gz.tbi results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/9/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.9.snv.sort.vcf.gz.tbi results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/10/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.10.snv.sort.vcf.gz.tbi results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/11/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.11.snv.sort.vcf.gz.tbi results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/12/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.12.snv.sort.vcf.gz.tbi results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/13/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.13.snv.sort.vcf.gz.tbi results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/14/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.14.snv.sort.vcf.gz.tbi results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/15/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.15.snv.sort.vcf.gz.tbi results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/16/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.16.snv.sort.vcf.gz.tbi results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/17-19/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.17-19.snv.sort.vcf.gz.tbi results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/20-25/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.20-25.snv.sort.vcf.gz.tbi; do
            ii=$(echo $i | perl -pe 's/\.tbi$//g'; );
            echo $ii >> results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/HYB-4Coriells-chip1-chip2-NA09677-SM--output truncated--
