DAY-EC activated.
DAY-EC activated.
__TIME__=2026-06-03T08:15:38Z
__SQUEUE_BEGIN__
JOBID|PARTITION|NAME|USER|ST|TIME|NODES|NODELIST(REASON)
57|i192bigmem|run_bclconvert_tile_shard-run_bclconvert_L003_0001_tiles0001-0008|ubuntu|CF|1:55|1|i192bigmem-dy-all-1
__SQUEUE_END__
__COUNTS__
fastq_count=0
done_count=0
bytes=10923
__LOG_TAIL_BEGIN__
missing_bcl_log
__LOG_TAIL_END__
__TMUX_TAIL_BEGIN__
clconvert_l003_8tile_tilesmoke_odirect_on_devshm_20260603T080931Z/benchmarks/bcl
convert_validate_inputs.bench.tsv
    reason: Missing output files: /fsx/run_dir_mounts/20260514_LH01106_0009_B23T
VLGLT4/fasts_from_bclconvert_l003_8tile_tilesmoke_odirect_on_devshm_20260603T080
931Z/normalized.SampleSheet.csv, /fsx/run_dir_mounts/20260514_LH01106_0009_B23TV
LGLT4/fasts_from_bclconvert_l003_8tile_tilesmoke_odirect_on_devshm_20260603T0809
31Z/logs/validated.ok
    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=


        set -euo pipefail
        mkdir -p /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from
_bclconvert_l003_8tile_tilesmoke_odirect_on_devshm_20260603T080931Z/logs /fsx/ru
n_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_8tile_t
ilesmoke_odirect_on_devshm_20260603T080931Z/tables
        : > /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclc
onvert_l003_8tile_tilesmoke_odirect_on_devshm_20260603T080931Z/logs/bclconvert_v
alidate_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_8tile_tilesmoke_odirect_on_
devshm_20260603T080931Z/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_8tile_tilesmoke_odirect_on_devshm_20260603T080931Z
/logs/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_8tile_tilesmoke_odirect_on_devshm_20260603T080931Z/logs/bc
lconvert_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_8tile_tilesmoke_odirect_on_devshm_20260603T080931Z/logs/bclco
nvert_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_8tile_tilesmo
ke_odirect_on_devshm_20260603T080931Z/daylily-omics-analysis/config/samples.tsv
\
          --normalized-out /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/
fasts_from_bclconvert_l003_8tile_tilesmoke_odirect_on_devshm_20260603T080931Z/no
rmalized.SampleSheet.csv \
          --rows-out /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_
from_bclconvert_l003_8tile_tilesmoke_odirect_on_devshm_20260603T080931Z/tables/s
amplesheet_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_8tile_tilesmoke_odirect_on_devshm_20260603T080931Z/logs
/bclconvert_validate_inputs.warnings.log \
          >> /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bcl
convert_l003_8tile_tilesmoke_odirect_on_devshm_20260603T080931Z/logs/bclconvert_
validate_inputs.log 2>&1
        touch /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bc
lconvert_l003_8tile_tilesmoke_odirect_on_devshm_20260603T080931Z/logs/validated.
ok

Activating conda environment: ../../../../resources/environments/conda/ubuntu/ip
-10-0-0-235/9d47d7d0d1fd2da30ac182cf088a614c_
[Wed Jun  3 08:13:43 2026]
Finished job 1.
1 of 5 steps (20%) done
Select jobs to execute...

[Wed Jun  3 08:13:43 2026]
rule run_bclconvert_tile_shard:
    input: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclco
nvert_l003_8tile_tilesmoke_odirect_on_devshm_20260603T080931Z/logs/validated.ok,
 /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003
_8tile_tilesmoke_odirect_on_devshm_20260603T080931Z/normalized.SampleSheet.csv
    output: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclc
onvert_l003_8tile_tilesmoke_odirect_on_devshm_20260603T080931Z/tile_reports/L003
/0001_tiles0001-0008/bclconvert.done, /fsx/run_dir_mounts/20260514_LH01106_0009_
B23TVLGLT4/fasts_from_bclconvert_l003_8tile_tilesmoke_odirect_on_devshm_20260603
T080931Z/tile_fastqs/L003/0001_tiles0001-0008/Reports/fastq_list.csv, /fsx/run_d
ir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_8tile_tile
smoke_odirect_on_devshm_20260603T080931Z/tile_fastqs/L003/0001_tiles0001-0008/Re
ports/Demultiplex_Stats.csv, /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT
4/fasts_from_bclconvert_l003_8tile_tilesmoke_odirect_on_devshm_20260603T080931Z/
tile_reports/L003/0001_tiles0001-0008/SampleSheet.csv
    log: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconv
ert_l003_8tile_tilesmoke_odirect_on_devshm_20260603T080931Z/logs/run_bclconvert.
L003.0001_tiles0001-0008.log
    jobid: 4
    benchmark: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_b
clconvert_l003_8tile_tilesmoke_odirect_on_devshm_20260603T080931Z/benchmarks/run
_bclconvert.L003.0001_tiles0001-0008.bench.tsv
    reason: Missing output files: /fsx/run_dir_mounts/20260514_LH01106_0009_B23T
VLGLT4/fasts_from_bclconvert_l003_8tile_tilesmoke_odirect_on_devshm_20260603T080
931Z/tile_reports/L003/0001_tiles0001-0008/bclconvert.done, /fsx/run_dir_mounts/
20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_8tile_tilesmoke_odir
ect_on_devshm_20260603T080931Z/tile_fastqs/L003/0001_tiles0001-0008/Reports/fast
q_list.csv, /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclc
onvert_l003_8tile_tilesmoke_odirect_on_devshm_20260603T080931Z/tile_fastqs/L003/
0001_tiles0001-0008/Reports/Demultiplex_Stats.csv; Input files updated by anothe
r job: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconver
t_l003_8tile_tilesmoke_odirect_on_devshm_20260603T080931Z/normalized.SampleSheet
.csv, /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert
_l003_8tile_tilesmoke_odirect_on_devshm_20260603T080931Z/logs/validated.ok
    wildcards: lane=L003, shard=0001_tiles0001-0008
    threads: 192
    resources: mem_mb=1200000, mem_mib=1144410, disk_mb=1000, disk_mib=954, tmpd
ir=<TBD>, threads=192, time=5440, partition=i192bigmem, vcpu=192, distribution=b
lock, exclusive=--exclusive, constraint=, exclude=, include=

TMPDIR=/dev/shm/dayoa_bclconvert_tmp bash workflow/scripts/run_bclconvert_lane.s
h docker://nfcore/bclconvert:4.0.3 /fsx/run_dir_mounts/20260514_LH01106_0009_B23
TVLGLT4 /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconve
rt_l003_8tile_tilesmoke_odirect_on_devshm_20260603T080931Z/tile_fastqs/L003/0001
_tiles0001-0008 /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_
bclconvert_l003_8tile_tilesmoke_odirect_on_devshm_20260603T080931Z/normalized.Sa
mpleSheet.csv 3 /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_
bclconvert_l003_8tile_tilesmoke_odirect_on_devshm_20260603T080931Z/tile_reports/
L003/0001_tiles0001-0008/SampleSheet.csv false false false 1 24 4 64 32 true tru
e 1000 '{"BarcodeMismatchesIndex1": "0", "BarcodeMismatchesIndex2": "0"}' '{}' _
_dayoa_no_force__ 192 /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts
_from_bclconvert_l003_8tile_tilesmoke_odirect_on_devshm_20260603T080931Z/logs/ru
n_bclconvert.L003.0001_tiles0001-0008.log /fsx/run_dir_mounts/20260514_LH01106_0
009_B23TVLGLT4/fasts_from_bclconvert_l003_8tile_tilesmoke_odirect_on_devshm_2026
0603T080931Z/tile_fastqs/L003/0001_tiles0001-0008/Reports/fastq_list.csv /fsx/ru
n_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_8tile_t
ilesmoke_odirect_on_devshm_20260603T080931Z/tile_fastqs/L003/0001_tiles0001-0008
/Reports/Demultiplex_Stats.csv /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLG
LT4/fasts_from_bclconvert_l003_8tile_tilesmoke_odirect_on_devshm_20260603T080931
Z/tile_reports/L003/0001_tiles0001-0008/bclconvert.done s_3_1101+s_3_1102+s_3_11
03+s_3_1104+s_3_1105+s_3_1106+s_3_1107+s_3_1108 /dev/shm/dayoa_bclconvert 650000
000000
Submitted job 4 with external jobid '57'.

__TMUX_TAIL_END__
