command_id=6e958c97-5e47-4778-ba68-fd3091cd0a75
DAY-EC activated.
DAY-EC activated.
__DATE__=2026-06-03T06:29:24+00:00
__PANE__
        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.
RETURN CODE: 1
__LIVE_ARGFIX2_EXIT__=1
[Dslu](DAYOA) dy-r --unlock --configfile config/bclconvert_l003_6shard_i192bigme
m_devshm_argfix.yaml; printf "__UNLOCK_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 --unlock --configfile 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
Unlocking working directory.

__LOCKS_AFTER_SEND__

