DAY-EC activated.
COMMAND_ID=5936527d-4b48-4de5-bb69-45f1a236d50c
DAY-EC activated.
DAY-EC activated.
timestamp_utc	2026-06-03T06:43:14Z
tmux_windows	1
tmux_panes	1
dryrun_exit	__DRYRUN_EMPTYDIRFIX_EXIT__=0
tile_shard_rule_count	6
full_lane_rule_count	0
other_lane_wildcard_count	0
partition_i192bigmem_hits	8
threads_192_hits	6
sentinel_hits	6
devshm_hits	12

== current squeue before live ==
JOBID|PARTITION|NAME|STATE|TIME|NODES|CPUS|MIN_MEMORY|NODELIST(REASON)

== tmux tail after launch ==
3_6shard_i192bigmem_devshm_emptydirfix_20260603T0642Z/lane_reports/L003/bclconve
rt.done, /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconv
ert_l003_6shard_i192bigmem_devshm_emptydirfix_20260603T0642Z/lane_fastqs/L003/Re
ports/fastq_list.csv, /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts
_from_bclconvert_l003_6shard_i192bigmem_devshm_emptydirfix_20260603T0642Z/lane_f
astqs/L003/Reports/Demultiplex_Stats.csv, /fsx/run_dir_mounts/20260514_LH01106_0
009_B23TVLGLT4/fasts_from_bclconvert_l003_6shard_i192bigmem_devshm_emptydirfix_2
0260603T0642Z/lane_reports/L003/SampleSheet.csv
    output: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclc
onvert_l003_6shard_i192bigmem_devshm_emptydirfix_20260603T0642Z/logs/bclconvert.
done
    log: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconv
ert_l003_6shard_i192bigmem_devshm_emptydirfix_20260603T0642Z/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_emptydirfix_20260603T0642Z/benchmarks/ru
n_bclconvert.lane_fastqs_ready.bench.tsv
    reason: Missing output files: /fsx/run_dir_mounts/20260514_LH01106_0009_B23T
VLGLT4/fasts_from_bclconvert_l003_6shard_i192bigmem_devshm_emptydirfix_20260603T
0642Z/logs/bclconvert.done; Input files updated by another job: /fsx/run_dir_mou
nts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shard_i192bigme
m_devshm_emptydirfix_20260603T0642Z/lane_fastqs/L003/Reports/Demultiplex_Stats.c
sv, /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l
003_6shard_i192bigmem_devshm_emptydirfix_20260603T0642Z/logs/validated.ok, /fsx/
run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shar
d_i192bigmem_devshm_emptydirfix_20260603T0642Z/lane_fastqs/L003/Reports/fastq_li
st.csv, /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconve
rt_l003_6shard_i192bigmem_devshm_emptydirfix_20260603T0642Z/lane_reports/L003/bc
lconvert.done, /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_b
clconvert_l003_6shard_i192bigmem_devshm_emptydirfix_20260603T0642Z/normalized.Sa
mpleSheet.csv, /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_b
clconvert_l003_6shard_i192bigmem_devshm_emptydirfix_20260603T0642Z/lane_reports/
L003/SampleSheet.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_emptydirfix_20260603T0642Z/logs
            : > /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_
bclconvert_l003_6shard_i192bigmem_devshm_emptydirfix_20260603T0642Z/logs/run_bcl
convert.lane_fastqs_ready.log
            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_emptydirfix_20260603T0642Z/lane_fastqs L0
03 >> /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert
_l003_6shard_i192bigmem_devshm_emptydirfix_20260603T0642Z/logs/run_bclconvert.la
ne_fastqs_ready.log
            touch /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_fro
m_bclconvert_l003_6shard_i192bigmem_devshm_emptydirfix_20260603T0642Z/logs/bclco
nvert.done


[Wed Jun  3 06:41:55 2026]
localrule produce_bclconvert_fastqs:
    input: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclco
nvert_l003_6shard_i192bigmem_devshm_emptydirfix_20260603T0642Z/logs/validated.ok
, /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l00
3_6shard_i192bigmem_devshm_emptydirfix_20260603T0642Z/logs/bclconvert.done
    output: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclc
onvert_l003_6shard_i192bigmem_devshm_emptydirfix_20260603T0642Z/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_emptydirfix_20260603T
0642Z/fastqs.complete, results/day/hg38/benchmarks/produce_bclconvert_fastqs.ben
ch.tsv; Input files updated by another job: /fsx/run_dir_mounts/20260514_LH01106
_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shard_i192bigmem_devshm_emptydirfix
_20260603T0642Z/logs/validated.ok, /fsx/run_dir_mounts/20260514_LH01106_0009_B23
TVLGLT4/fasts_from_bclconvert_l003_6shard_i192bigmem_devshm_emptydirfix_20260603
T0642Z/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_emptydirfix_20260603T0642Z/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_EMPTYDIRFIX_EXIT__=0
[Dslu](DAYOA) dy-r produce_bclconvert_fastqs -p -k -j 10 --rerun-triggers mtime
--configfile config/bclconvert_l003_6shard_i192bigmem_devshm_emptydirfix.yaml; e
cho __LIVE_EMPTYDIRFIX_EXIT__=$?
Your config files in /fsx/analysis_results/dyec0602bcl/bcl_l003_6shard_i192bigme
m_devshm_emptydirfix_20260603T0642Z/daylily-omics-analysis/config/day_profiles/s
lurm are newer than the templates. clear 2 go.
Executing: snakemake --profile=/fsx/analysis_results/dyec0602bcl/bcl_l003_6shard
_i192bigmem_devshm_emptydirfix_20260603T0642Z/daylily-omics-analysis/config/day_
profiles/slurm produce_bclconvert_fastqs -p -k -j 10 --rerun-triggers mtime --co
nfigfile config/bclconvert_l003_6shard_i192bigmem_devshm_emptydirfix.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_emptydirfix_20260603T0642Z/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_emptydirfix_20260603T0642Z/daylily-omics-analysis/config/day_pr
ofiles/slurm/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_emptydirfix_20260603T0642Z/daylily-omic
s-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_emptydirfix_20260603T0642Z/daylily-omics-
analysis/config/units.tsv
Building DAG of jobs...


== squeue after launch ==
JOBID|PARTITION|NAME|STATE|TIME|NODES|CPUS|MIN_MEMORY|NODELIST(REASON)

