command_id=95aac924-b6f4-4090-bf48-67c68f1c85ef
DAY-EC activated.
DAY-EC activated.
__DATE_START__=2026-06-03T04:31:39+00:00
__TMUX_TAIL_INITIAL__
_reports/L003/SampleSheet.csv
    log: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconv
ert_l003_6shard_i192bigmem_devshm/logs/merge_bclconvert_tile_shards.L003.log
    jobid: 3
    benchmark: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_b
clconvert_l003_6shard_i192bigmem_devshm/benchmarks/merge_bclconvert_tile_shards.
L003.bench.tsv
    reason: Missing output files: /fsx/run_dir_mounts/20260514_LH01106_0009_B23T
VLGLT4/fasts_from_bclconvert_l003_6shard_i192bigmem_devshm/lane_reports/L003/Sam
pleSheet.csv, /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bc
lconvert_l003_6shard_i192bigmem_devshm/lane_fastqs/L003/Reports/fastq_list.csv,
/fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_
6shard_i192bigmem_devshm/lane_fastqs/L003/Reports/Demultiplex_Stats.csv, /fsx/ru
n_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shard_
i192bigmem_devshm/lane_reports/L003/bclconvert.done; Input files updated by anot
her job: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconv
ert_l003_6shard_i192bigmem_devshm/tile_fastqs/L003/0003_tiles0263-0393/Reports/D
emultiplex_Stats.csv, /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts
_from_bclconvert_l003_6shard_i192bigmem_devshm/tile_fastqs/L003/0002_tiles0132-0
262/Reports/Demultiplex_Stats.csv, /fsx/run_dir_mounts/20260514_LH01106_0009_B23
TVLGLT4/fasts_from_bclconvert_l003_6shard_i192bigmem_devshm/tile_fastqs/L003/000
1_tiles0001-0131/Reports/Demultiplex_Stats.csv, /fsx/run_dir_mounts/20260514_LH0
1106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shard_i192bigmem_devshm/tile_fa
stqs/L003/0006_tiles0655-0784/Reports/fastq_list.csv, /fsx/run_dir_mounts/202605
14_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shard_i192bigmem_devshm/n
ormalized.SampleSheet.csv, /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/
fasts_from_bclconvert_l003_6shard_i192bigmem_devshm/tile_reports/L003/0003_tiles
0263-0393/bclconvert.done, /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/
fasts_from_bclconvert_l003_6shard_i192bigmem_devshm/tile_fastqs/L003/0003_tiles0
263-0393/Reports/fastq_list.csv, /fsx/run_dir_mounts/20260514_LH01106_0009_B23TV
LGLT4/fasts_from_bclconvert_l003_6shard_i192bigmem_devshm/tile_fastqs/L003/0001_
tiles0001-0131/Reports/fastq_list.csv, /fsx/run_dir_mounts/20260514_LH01106_0009
_B23TVLGLT4/fasts_from_bclconvert_l003_6shard_i192bigmem_devshm/tile_fastqs/L003
/0004_tiles0394-0524/Reports/Demultiplex_Stats.csv, /fsx/run_dir_mounts/20260514
_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shard_i192bigmem_devshm/til
e_fastqs/L003/0006_tiles0655-0784/Reports/Demultiplex_Stats.csv, /fsx/run_dir_mo
unts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shard_i192bigm
em_devshm/tile_fastqs/L003/0004_tiles0394-0524/Reports/fastq_list.csv, /fsx/run_
dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shard_i1
92bigmem_devshm/tile_reports/L003/0001_tiles0001-0131/bclconvert.done, /fsx/run_
dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shard_i1
92bigmem_devshm/tile_reports/L003/0005_tiles0525-0654/bclconvert.done, /fsx/run_
dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shard_i1
92bigmem_devshm/tile_reports/L003/0002_tiles0132-0262/bclconvert.done, /fsx/run_
dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shard_i1
92bigmem_devshm/tile_reports/L003/0006_tiles0655-0784/bclconvert.done, /fsx/run_
dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shard_i1
92bigmem_devshm/tile_fastqs/L003/0002_tiles0132-0262/Reports/fastq_list.csv, /fs
x/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6sh
ard_i192bigmem_devshm/tile_reports/L003/0004_tiles0394-0524/bclconvert.done, /fs
x/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6sh
ard_i192bigmem_devshm/tile_fastqs/L003/0005_tiles0525-0654/Reports/Demultiplex_S
tats.csv, /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclcon
vert_l003_6shard_i192bigmem_devshm/tile_fastqs/L003/0005_tiles0525-0654/Reports/
fastq_list.csv
    wildcards: lane=L003
    resources: mem_mb=3000, mem_mib=2862, disk_mb=1000, disk_mib=954, tmpdir=<TB
D>, threads=1, time=5440, partition=i192bigmem, vcpu=1, distribution=block, excl
usive=, constraint=, exclude=, include=

python workflow/scripts/merge_bclconvert_tile_shards.py --tile-fastq-root /fsx/r
un_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shard
_i192bigmem_devshm/tile_fastqs --lane-output-dir /fsx/run_dir_mounts/20260514_LH
01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shard_i192bigmem_devshm/lane_f
astqs/L003 --report-dir /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fas
ts_from_bclconvert_l003_6shard_i192bigmem_devshm/lane_fastqs/L003/Reports --lane
 L003 --shards 0001_tiles0001-0131,0002_tiles0132-0262,0003_tiles0263-0393,0004_
tiles0394-0524,0005_tiles0525-0654,0006_tiles0655-0784 --merge-fastqs false --sa
mple-sheet /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclco
nvert_l003_6shard_i192bigmem_devshm/normalized.SampleSheet.csv --lane-sample-she
et /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l0
03_6shard_i192bigmem_devshm/lane_reports/L003/SampleSheet.csv --done /fsx/run_di
r_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shard_i192
bigmem_devshm/lane_reports/L003/bclconvert.done --log /fsx/run_dir_mounts/202605
14_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shard_i192bigmem_devshm/l
ogs/merge_bclconvert_tile_shards.L003.log >> /fsx/run_dir_mounts/20260514_LH0110
6_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shard_i192bigmem_devshm/logs/merge
_bclconvert_tile_shards.L003.log 2>&1 && test -s /fsx/run_dir_mounts/20260514_LH
01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shard_i192bigmem_devshm/lane_f
astqs/L003/Reports/fastq_list.csv && test -s /fsx/run_dir_mounts/20260514_LH0110
6_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shard_i192bigmem_devshm/lane_fastq
s/L003/Reports/Demultiplex_Stats.csv

[Wed Jun  3 04:29:20 2026]
localrule run_bclconvert:
    input: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclco
nvert_l003_6shard_i192bigmem_devshm/logs/validated.ok, /fsx/run_dir_mounts/20260
514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shard_i192bigmem_devshm/
normalized.SampleSheet.csv, /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4
/fasts_from_bclconvert_l003_6shard_i192bigmem_devshm/lane_reports/L003/bclconver
t.done, /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconve
rt_l003_6shard_i192bigmem_devshm/lane_fastqs/L003/Reports/fastq_list.csv, /fsx/r
un_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shard
_i192bigmem_devshm/lane_fastqs/L003/Reports/Demultiplex_Stats.csv, /fsx/run_dir_
mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shard_i192bi
gmem_devshm/lane_reports/L003/SampleSheet.csv
    output: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclc
onvert_l003_6shard_i192bigmem_devshm/logs/bclconvert.done
    log: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconv
ert_l003_6shard_i192bigmem_devshm/logs/run_bclconvert.lane_fastqs_ready.log
    jobid: 2
    benchmark: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_b
clconvert_l003_6shard_i192bigmem_devshm/benchmarks/run_bclconvert.lane_fastqs_re
ady.bench.tsv
    reason: Missing output files: /fsx/run_dir_mounts/20260514_LH01106_0009_B23T
VLGLT4/fasts_from_bclconvert_l003_6shard_i192bigmem_devshm/logs/bclconvert.done;
 Input files updated by another job: /fsx/run_dir_mounts/20260514_LH01106_0009_B
23TVLGLT4/fasts_from_bclconvert_l003_6shard_i192bigmem_devshm/logs/validated.ok,
 /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003
_6shard_i192bigmem_devshm/lane_reports/L003/SampleSheet.csv, /fsx/run_dir_mounts
/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shard_i192bigmem_d
evshm/normalized.SampleSheet.csv, /fsx/run_dir_mounts/20260514_LH01106_0009_B23T
VLGLT4/fasts_from_bclconvert_l003_6shard_i192bigmem_devshm/lane_fastqs/L003/Repo
rts/fastq_list.csv, /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_f
rom_bclconvert_l003_6shard_i192bigmem_devshm/lane_reports/L003/bclconvert.done,
/fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_
6shard_i192bigmem_devshm/lane_fastqs/L003/Reports/Demultiplex_Stats.csv
    resources: mem_mb=3000, mem_mib=2862, disk_mb=1000, disk_mib=954, tmpdir=/de
v/shm/dayoa_bclconvert_tmp, threads=1, time=5440, partition=i192bigmem, vcpu=1,
distribution=block, exclusive=, constraint=, exclude=, include=


            set -euo pipefail
            mkdir -p /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_
from_bclconvert_l003_6shard_i192bigmem_devshm/logs
            : > /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_
bclconvert_l003_6shard_i192bigmem_devshm/logs/run_bclconvert.lane_fastqs_ready.l
og
            printf 'merge_lane_fastqs=false; lane FASTQs remain under %s for lan
es %s\n' \
              /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bc
lconvert_l003_6shard_i192bigmem_devshm/lane_fastqs L003 >> /fsx/run_dir_mounts/2
0260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shard_i192bigmem_dev
shm/logs/run_bclconvert.lane_fastqs_ready.log
            touch /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_fro
m_bclconvert_l003_6shard_i192bigmem_devshm/logs/bclconvert.done


[Wed Jun  3 04:29:20 2026]
localrule produce_bclconvert_fastqs:
    input: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclco
nvert_l003_6shard_i192bigmem_devshm/logs/validated.ok, /fsx/run_dir_mounts/20260
514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shard_i192bigmem_devshm/
logs/bclconvert.done
    output: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclc
onvert_l003_6shard_i192bigmem_devshm/fastqs.complete
    log: results/day/hg38/logs/produce_bclconvert_fastqs.log
    jobid: 0
    benchmark: results/day/hg38/benchmarks/produce_bclconvert_fastqs.bench.tsv
    reason: Missing output files: /fsx/run_dir_mounts/20260514_LH01106_0009_B23T
VLGLT4/fasts_from_bclconvert_l003_6shard_i192bigmem_devshm/fastqs.complete, resu
lts/day/hg38/benchmarks/produce_bclconvert_fastqs.bench.tsv; Input files updated
 by another job: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from
_bclconvert_l003_6shard_i192bigmem_devshm/logs/validated.ok, /fsx/run_dir_mounts
/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shard_i192bigmem_d
evshm/logs/bclconvert.done
    resources: mem_mb=3000, mem_mib=2862, disk_mb=1000, disk_mib=954, tmpdir=/de
v/shm, threads=1, time=5440, partition=i192,i128,i192mem, vcpu=1, distribution=b
lock, exclusive=, constraint=, exclude=, include=

touch /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert
_l003_6shard_i192bigmem_devshm/fastqs.complete
Job stats:
job                             count    min threads    max threads
----------------------------  -------  -------------  -------------
bclconvert_validate_inputs          1              1              1
merge_bclconvert_tile_shards        1              1              1
produce_bclconvert_fastqs           1              1              1
run_bclconvert                      1              1              1
run_bclconvert_tile_shard           6            192            192
total                              10              1            192

Reasons:
    (check individual jobs above for details)
    input files updated by another job:
        merge_bclconvert_tile_shards, produce_bclconvert_fastqs, run_bclconvert,
 run_bclconvert_tile_shard
    missing output files:
        bclconvert_validate_inputs, merge_bclconvert_tile_shards, produce_bclcon
vert_fastqs, run_bclconvert, run_bclconvert_tile_shard

This was a dry-run (flag -n). The order of jobs does not reflect the order of ex
ecution.
RETURN CODE: 0
__DRYRUN_EXIT__=0
[Dslu](DAYOA) dy-r produce_bclconvert_fastqs -p -k -j 10 --rerun-triggers mtime
--configfile config/bclconvert_l003_6shard_i192bigmem_devshm.yaml; printf '__LIV
E_EXIT__=%s\n' "$?"
Your config files in /fsx/analysis_results/dyec0602bcl/bcl_l003_6shard_i192bigme
m_devshm_20260603T041747Z/daylily-omics-analysis/config/day_profiles/slurm are n
ewer than the templates. clear 2 go.
Executing: snakemake --profile=/fsx/analysis_results/dyec0602bcl/bcl_l003_6shard
_i192bigmem_devshm_20260603T041747Z/daylily-omics-analysis/config/day_profiles/s
lurm produce_bclconvert_fastqs -p -k -j 10 --rerun-triggers mtime --configfile c
onfig/bclconvert_l003_6shard_i192bigmem_devshm.yaml
Config file config/global.yaml is extended by additional config specified via th
e command line.
loading global: /fsx/analysis_results/dyec0602bcl/bcl_l003_6shard_i192bigmem_dev
shm_20260603T041747Z/daylily-omics-analysis/config/global_AWSPC.yaml
Config file config/global_AWSPC.yaml is extended by additional config specified
via the command line.
loading profile rule_config: /fsx/analysis_results/dyec0602bcl/bcl_l003_6shard_i
192bigmem_devshm_20260603T041747Z/daylily-omics-analysis/config/day_profiles/slu
rm/rule_config.yaml
Config file config/day_profiles/slurm/rule_config.yaml is extended by additional
 config specified via the command line.
INFO::: The genome build hg38 is supported.  The genome build prefix is 'chr''.
...WARNING: No aligners set in the config.
aligners (final): []
...INFO: No dedupers set in config. Defaulting to na (no dedup).
deduper (final): [na]
...WARNING: No snv_callers set in the config.
SNV Callers (final): []
Somatic SNV Callers:[senttn]
... WARNING: No sv_callers set in the config.
SV Callers (final): []
A    N   A   L  Y S I S    SAMPLE TABLE DETECTED ::: /fsx/analysis_results/dyec0
602bcl/bcl_l003_6shard_i192bigmem_devshm_20260603T041747Z/daylily-omics-analysis
/config/samples.tsv
A    N   A   L  Y S I S    UNIT TABLE DETECTED ::: /fsx/analysis_results/dyec060
2bcl/bcl_l003_6shard_i192bigmem_devshm_20260603T041747Z/daylily-omics-analysis/c
onfig/units.tsv
Building DAG of jobs...

__DATE_END__=2026-06-03T04:31:44+00:00

