command_id=2afb6d04-08e4-43d1-bee7-0c7b8fa3955f
DAY-EC activated.
DAY-EC activated.
__DATE__=2026-06-03T06:28:29+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 1532/2000, 545092 bytes] %4 (active)
__PANE__
sx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6s
hard_i192bigmem_devshm_argfix_20260603T0620Z/normalized.SampleSheet.csv, /fsx/ru
n_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shard_
i192bigmem_devshm_argfix_20260603T0620Z/tables/samplesheet_rows.tsv
    log: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconv
ert_l003_6shard_i192bigmem_devshm_argfix_20260603T0620Z/logs/bclconvert_validate
_inputs.log (check log file(s) for error details)
    conda-env: /fsx/resources/environments/conda/ubuntu/ip-10-0-0-235/9d47d7d0d1
fd2da30ac182cf088a614c_
    shell:

        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_di
r_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shard_i192
bigmem_devshm_argfix_20260603T0620Z/tables
        : > /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclc
onvert_l003_6shard_i192bigmem_devshm_argfix_20260603T0620Z/logs/bclconvert_valid
ate_inputs.log
        if [ -z /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4 ]; then
            echo "bclconvert.run_dir is required" >> /fsx/run_dir_mounts/2026051
4_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shard_i192bigmem_devshm_ar
gfix_20260603T0620Z/logs/bclconvert_validate_inputs.log
            exit 2
        fi
        if [ ! -d /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4 ]; then
            echo "bclconvert.run_dir does not exist: /fsx/run_dir_mounts/2026051
4_LH01106_0009_B23TVLGLT4" >> /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGL
T4/fasts_from_bclconvert_l003_6shard_i192bigmem_devshm_argfix_20260603T0620Z/log
s/bclconvert_validate_inputs.log
            exit 2
        fi
        if [ "true" = "false" ]; then
            echo "keep_undetermined_fastqs=false is unsupported for the bclconve
rt bootstrap path" >> /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts
_from_bclconvert_l003_6shard_i192bigmem_devshm_argfix_20260603T0620Z/logs/bclcon
vert_validate_inputs.log
            exit 2
        fi
        bcl_extra_args=
        if [ -n "$bcl_extra_args" ]; then
            echo "bclconvert.extra_args is not supported in this shell-only boot
strap workflow" >> /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_fr
om_bclconvert_l003_6shard_i192bigmem_devshm_argfix_20260603T0620Z/logs/bclconver
t_validate_inputs.log
            exit 2
        fi
        python workflow/scripts/parse_bclconvert_samplesheet.py \
          --sample-sheet /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/Sa
mpleSheet.csv \
          --samples-tsv /fsx/analysis_results/dyec0602bcl/bcl_l003_6shard_i192bi
gmem_devshm_argfix_20260603T0620Z/daylily-omics-analysis/config/samples.tsv \
          --normalized-out /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/
fasts_from_bclconvert_l003_6shard_i192bigmem_devshm_argfix_20260603T0620Z/normal
ized.SampleSheet.csv \
          --rows-out /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_
from_bclconvert_l003_6shard_i192bigmem_devshm_argfix_20260603T0620Z/tables/sampl
esheet_rows.tsv \
          --runtime-version 4.0.3 \
          --sampleproject-subdirectories false \
          --warnings-out /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fa
sts_from_bclconvert_l003_6shard_i192bigmem_devshm_argfix_20260603T0620Z/logs/bcl
convert_validate_inputs.warnings.log \
          >> /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bcl
convert_l003_6shard_i192bigmem_devshm_argfix_20260603T0620Z/logs/bclconvert_vali
date_inputs.log 2>&1
        touch /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bc
lconvert_l003_6shard_i192bigmem_devshm_argfix_20260603T0620Z/logs/validated.ok

        (one of the commands exited with non-zero exit code; note that snakemake
 uses bash strict mode!)

Exiting because a job execution failed. Look above for error message

        Womp Womp.  something went awry----
RETURN CODE: 1
__LIVE_ARGFIX_EXIT__=1
[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_ARGFIX2_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]
... 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_argfix_20260603T0620Z/daylily-omics-ana
lysis/config/samples.tsv
A    N   A   L  Y S I S    UNIT TABLE DETECTED ::: /fsx/analysis_results/dyec060
2bcl/bcl_l003_6shard_i192bigmem_devshm_argfix_20260603T0620Z/daylily-omics-analy
sis/config/units.tsv
Building DAG of jobs...
LockException:
Error: Directory cannot be locked. Please make sure that no other Snakemake proc
ess is trying to create the same files in the following directory:
/fsx/analysis_results/dyec0602bcl/bcl_l003_6shard_i192bigmem_devshm_argfix_20260
603T0620Z/daylily-omics-analysis
If you are sure that no other instances of snakemake are running on this directo
ry, the remaining lock was likely caused by a kill signal or a power loss. It ca
n be removed with the --unlock argument.

__SQUEUE_AFTER_SEND__
             JOBID    PARTITION                                               NAME    STATE       TIME      NODES NODELIST(REASON)

