command_id=98519db0-61df-4d2a-a0c2-b94c334682df
DAY-EC activated.
DAY-EC activated.
__DATE__=2026-06-03T06:26:23+00:00
__SQUEUE__
             JOBID    PARTITION                                                       NAME      STATE       TIME      NODES NODELIST(REASON)
__SINFO__
PARTITION AVAIL NODES STATE CPUS MEMORY NODELIST REASON
i192bigmem up 1 idle~ 192 1494220 i192bigmem-dy-all-1 none
bcl2fq up 8 idle~ 48+ 373555+ bcl2fq-dy-nvme48-[1-4],bcl2fq-dy-nvme96-[1-4] Enabling node since insufficient capacity timeout expired
bcl2fq up 8 idle~ 64+ 498073+ bcl2fq-dy-nvme64-[1-4],bcl2fq-dy-nvme128-[1-4] Scheduler health check failed
__TMUX_TAIL__
_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

Activating conda environment: ../../../../resources/environments/conda/ubuntu/ip
-10-0-0-235/9d47d7d0d1fd2da30ac182cf088a614c_
[Wed Jun  3 06:25:49 2026]
Error in rule bclconvert_validate_inputs:
    jobid: 1
    input: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/SampleSheet.csv,
 /fsx/analysis_results/dyec0602bcl/bcl_l003_6shard_i192bigmem_devshm_argfix_2026
0603T0620Z/daylily-omics-analysis/config/samples.tsv
    output: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclc
onvert_l003_6shard_i192bigmem_devshm_argfix_20260603T0620Z/logs/validated.ok, /f
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)
__DEST_COUNTS__
120K	/fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shard_i192bigmem_devshm_argfix_20260603T0620Z
fastq_count=0
done_count=0
bench_count=0
fastq_list_count=0
__RUN_LOGS_HEAD__
__SLURM_LOGS__

