DAY-EC activated.
DAY-EC activated.
marks/run_bclconvert.lane_fastqs_ready.bench.tsv
    reason: Missing output files: /fsx/run_dir_mounts/20260514_LH01106_0009_B23T
VLGLT4/fasts_from_bclconvert_l003_8tile_tilesmoke_odirect_on_fsx_scratch_tmp_202
60603T082415Z/logs/bclconvert.done; Input files updated by another job: /fsx/run
_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_8tile_ti
lesmoke_odirect_on_fsx_scratch_tmp_20260603T082415Z/normalized.SampleSheet.csv,
/fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_
8tile_tilesmoke_odirect_on_fsx_scratch_tmp_20260603T082415Z/lane_reports/L003/bc
lconvert.done, /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_b
clconvert_l003_8tile_tilesmoke_odirect_on_fsx_scratch_tmp_20260603T082415Z/logs/
validated.ok, /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bc
lconvert_l003_8tile_tilesmoke_odirect_on_fsx_scratch_tmp_20260603T082415Z/lane_f
astqs/L003/Reports/fastq_list.csv, /fsx/run_dir_mounts/20260514_LH01106_0009_B23
TVLGLT4/fasts_from_bclconvert_l003_8tile_tilesmoke_odirect_on_fsx_scratch_tmp_20
260603T082415Z/lane_reports/L003/SampleSheet.csv, /fsx/run_dir_mounts/20260514_L
H01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_8tile_tilesmoke_odirect_on_fsx
_scratch_tmp_20260603T082415Z/lane_fastqs/L003/Reports/Demultiplex_Stats.csv
    resources: mem_mb=3000, mem_mib=2862, disk_mb=1000, disk_mib=954, tmpdir=/fs
x/scratch/tmp/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_8tile_tilesmoke_odirect_on_fsx_scratch_tmp_20260603T082415Z
/logs
            : > /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_
bclconvert_l003_8tile_tilesmoke_odirect_on_fsx_scratch_tmp_20260603T082415Z/logs
/run_bclconvert.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_8tile_tilesmoke_odirect_on_fsx_scratch_tmp_20260603T082415Z/lane_f
astqs L003 >> /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bc
lconvert_l003_8tile_tilesmoke_odirect_on_fsx_scratch_tmp_20260603T082415Z/logs/r
un_bclconvert.lane_fastqs_ready.log
            touch /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_fro
m_bclconvert_l003_8tile_tilesmoke_odirect_on_fsx_scratch_tmp_20260603T082415Z/lo
gs/bclconvert.done


[Wed Jun  3 08:27:18 2026]
localrule produce_bclconvert_fastqs:
    input: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclco
nvert_l003_8tile_tilesmoke_odirect_on_fsx_scratch_tmp_20260603T082415Z/logs/vali
dated.ok, /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclcon
vert_l003_8tile_tilesmoke_odirect_on_fsx_scratch_tmp_20260603T082415Z/logs/bclco
nvert.done
    output: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclc
onvert_l003_8tile_tilesmoke_odirect_on_fsx_scratch_tmp_20260603T082415Z/fastqs.c
omplete
    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_8tile_tilesmoke_odirect_on_fsx_scratch_tmp_202
60603T082415Z/fastqs.complete, results/day/hg38/benchmarks/produce_bclconvert_fa
stqs.bench.tsv; Input files updated by another job: /fsx/run_dir_mounts/20260514
_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_8tile_tilesmoke_odirect_on_f
sx_scratch_tmp_20260603T082415Z/logs/bclconvert.done, /fsx/run_dir_mounts/202605
14_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_8tile_tilesmoke_odirect_on
_fsx_scratch_tmp_20260603T082415Z/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=

touch /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert
_l003_8tile_tilesmoke_odirect_on_fsx_scratch_tmp_20260603T082415Z/fastqs.complet
e
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           1            192            192
total                               5              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
__DRY_FSXSCRATCH_ODIRECT_RC__0
[Dslu](DAYOA) dy-r produce_bclconvert_fastqs -p -k -j 10 -T 0 --rerun-triggers m
time --configfile config/bclconvert_l003_8tile_tilesmoke_odirect_on_fsx_scratch_
tmp_20260603T082415Z.yaml; echo __LIVE_FSXSCRATCH_ODIRECT_RC__$?
Your config files in /fsx/analysis_results/dyec0602bcl/bcl_l003_8tile_tilesmoke_
odirect_on_fsx_scratch_tmp_20260603T082415Z/daylily-omics-analysis/config/day_pr
ofiles/slurm are newer than the templates. clear 2 go.
Executing: snakemake --profile=/fsx/analysis_results/dyec0602bcl/bcl_l003_8tile_
tilesmoke_odirect_on_fsx_scratch_tmp_20260603T082415Z/daylily-omics-analysis/con
fig/day_profiles/slurm produce_bclconvert_fastqs -p -k -j 10 -T 0 --rerun-trigge
rs mtime --configfile config/bclconvert_l003_8tile_tilesmoke_odirect_on_fsx_scra
tch_tmp_20260603T082415Z.yaml

JOBID|PARTITION|NAME|USER|ST|TIME|NODES|NODELIST(REASON)
