command_id=edfce2c8-7db4-4c45-9f24-5e2cfb579447
DAY-EC activated.
DAY-EC activated.
__DATE__=2026-06-03T06:25:42+00:00
__SQUEUE_BEFORE__
             JOBID    PARTITION                                               NAME    STATE       TIME      NODES NODELIST(REASON)
0: bash* (1 panes) [80x24] [layout b261,80x24,0,0,4] @4 (active)
0: [80x24] [history 1136/2000, 410320 bytes] %4 (active)
__PANE__
-s /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l0
03_6shard_i192bigmem_devshm_argfix_20260603T0620Z/lane_fastqs/L003/Reports/Demul
tiplex_Stats.csv

[Wed Jun  3 06:23:55 2026]
localrule run_bclconvert:
    input: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclco
nvert_l003_6shard_i192bigmem_devshm_argfix_20260603T0620Z/logs/validated.ok, /fs
x/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6sh
ard_i192bigmem_devshm_argfix_20260603T0620Z/normalized.SampleSheet.csv, /fsx/run
_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shard_i
192bigmem_devshm_argfix_20260603T0620Z/lane_reports/L003/bclconvert.done, /fsx/r
un_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shard
_i192bigmem_devshm_argfix_20260603T0620Z/lane_fastqs/L003/Reports/fastq_list.csv
, /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l00
3_6shard_i192bigmem_devshm_argfix_20260603T0620Z/lane_fastqs/L003/Reports/Demult
iplex_Stats.csv, /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from
_bclconvert_l003_6shard_i192bigmem_devshm_argfix_20260603T0620Z/lane_reports/L00
3/SampleSheet.csv
    output: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclc
onvert_l003_6shard_i192bigmem_devshm_argfix_20260603T0620Z/logs/bclconvert.done
    log: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconv
ert_l003_6shard_i192bigmem_devshm_argfix_20260603T0620Z/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_argfix_20260603T0620Z/benchmarks/run_bcl
convert.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_argfix_20260603T0620Z
/logs/bclconvert.done; Input files updated by another job: /fsx/run_dir_mounts/2
0260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shard_i192bigmem_dev
shm_argfix_20260603T0620Z/lane_fastqs/L003/Reports/fastq_list.csv, /fsx/run_dir_
mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shard_i192bi
gmem_devshm_argfix_20260603T0620Z/lane_reports/L003/bclconvert.done, /fsx/run_di
r_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shard_i192
bigmem_devshm_argfix_20260603T0620Z/lane_fastqs/L003/Reports/Demultiplex_Stats.c
sv, /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l
003_6shard_i192bigmem_devshm_argfix_20260603T0620Z/lane_reports/L003/SampleSheet
.csv, /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert
_l003_6shard_i192bigmem_devshm_argfix_20260603T0620Z/logs/validated.ok, /fsx/run
_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shard_i
192bigmem_devshm_argfix_20260603T0620Z/normalized.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_argfix_20260603T0620Z/logs
            : > /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_
bclconvert_l003_6shard_i192bigmem_devshm_argfix_20260603T0620Z/logs/run_bclconve
rt.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_argfix_20260603T0620Z/lane_fastqs L003 >>
 /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003
_6shard_i192bigmem_devshm_argfix_20260603T0620Z/logs/run_bclconvert.lane_fastqs_
ready.log
            touch /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_fro
m_bclconvert_l003_6shard_i192bigmem_devshm_argfix_20260603T0620Z/logs/bclconvert
.done


[Wed Jun  3 06:23:55 2026]
localrule produce_bclconvert_fastqs:
    input: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclco
nvert_l003_6shard_i192bigmem_devshm_argfix_20260603T0620Z/logs/validated.ok, /fs
x/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6sh
ard_i192bigmem_devshm_argfix_20260603T0620Z/logs/bclconvert.done
    output: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclc
onvert_l003_6shard_i192bigmem_devshm_argfix_20260603T0620Z/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_argfix_20260603T0620Z
/fastqs.complete, results/day/hg38/benchmarks/produce_bclconvert_fastqs.bench.ts
v; Input files updated by another job: /fsx/run_dir_mounts/20260514_LH01106_0009
_B23TVLGLT4/fasts_from_bclconvert_l003_6shard_i192bigmem_devshm_argfix_20260603T
0620Z/logs/validated.ok, /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fa
sts_from_bclconvert_l003_6shard_i192bigmem_devshm_argfix_20260603T0620Z/logs/bcl
convert.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_argfix_20260603T0620Z/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_ARGFIX_EXIT__=0
[Dslu](DAYOA) dy-r produce_bclconvert_fastqs -p -k -j 10 --rerun-triggers mtime
--configfile config/bclconvert_l003_6shard_i192bigmem_devshm_argfix.yaml; printf
 "__LIVE_ARGFIX_EXIT__=%s\n" "$?"
Your config files in /fsx/analysis_results/dyec0602bcl/bcl_l003_6shard_i192bigme
m_devshm_argfix_20260603T0620Z/daylily-omics-analysis/config/day_profiles/slurm
are newer than the templates. clear 2 go.
Executing: snakemake --profile=/fsx/analysis_results/dyec0602bcl/bcl_l003_6shard
_i192bigmem_devshm_argfix_20260603T0620Z/daylily-omics-analysis/config/day_profi
les/slurm produce_bclconvert_fastqs -p -k -j 10 --rerun-triggers mtime --configf
ile config/bclconvert_l003_6shard_i192bigmem_devshm_argfix.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_argfix_20260603T0620Z/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_argfix_20260603T0620Z/daylily-omics-analysis/config/day_profile
s/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]

__SQUEUE_AFTER_SEND__
             JOBID    PARTITION                                               NAME    STATE       TIME      NODES NODELIST(REASON)

