command_id=1dc2901d-70ee-4b33-9dd8-8621907cdb05
DAY-EC activated.
DAY-EC activated.
__DATE__=2026-06-03T04:21:33+00:00
__QUEUE_SHORT__
JOBID              PARTITION    NAME                                                         USER     ST TIME       NODES  NODELIST(REASON)
10                 bcl2fq       run_bclconvert_lane-run_bclconvert_L003                      ubuntu   PD 0:00       1      (BeginTime)
9                  bcl2fq       run_bclconvert_lane-run_bclconvert_L005                      ubuntu   PD 0:00       1      (ReqNodeNotAvail, UnavailableNodes:bcl2fq-dy-nvme48-[1-4],bcl2fq-dy-nvme64-[1-2])
8                  bcl2fq       run_bclconvert_lane-run_bclconvert_L004                      ubuntu   PD 0:00       1      (None)
7                  bcl2fq       run_bclconvert_lane-run_bclconvert_L007                      ubuntu   PD 0:00       1      (ReqNodeNotAvail, UnavailableNodes:bcl2fq-dy-nvme48-[1-4],bcl2fq-dy-nvme64-[1-2])
6                  bcl2fq       run_bclconvert_lane-run_bclconvert_L002                      ubuntu   PD 0:00       1      (ReqNodeNotAvail, UnavailableNodes:bcl2fq-dy-nvme48-[1-4],bcl2fq-dy-nvme64-[1-2])
5                  bcl2fq       run_bclconvert_lane-run_bclconvert_L006                      ubuntu   PD 0:00       1      (ReqNodeNotAvail, UnavailableNodes:bcl2fq-dy-nvme48-[1-4],bcl2fq-dy-nvme64-[1-2])
4                  bcl2fq       run_bclconvert_lane-run_bclconvert_L008                      ubuntu   PD 0:00       1      (ReqNodeNotAvail, UnavailableNodes:bcl2fq-dy-nvme48-[1-4],bcl2fq-dy-nvme64-[1-2])
3                  bcl2fq       run_bclconvert_lane-run_bclconvert_L003                      ubuntu   PD 0:00       1      (None)
2                  bcl2fq       run_bclconvert_lane-run_bclconvert_L001                      ubuntu   PD 0:00       1      (None)
1                  bcl2fq       bcl2fq_scratch_to_dra                                        ubuntu   PD 0:00       1      (None)
__TMUX_SESSIONS__
bcl2fq_scratch_dra_20260603T011121Z: 1 windows (created Wed Jun  3 01:18:13 2026)
dayoa_bcl2fq_scratch_dra_20260603: 1 windows (created Wed Jun  3 03:05:52 2026)
dayoa_bcl_l003_bcl2fq_scratch_20260603: 1 windows (created Wed Jun  3 03:46:04 2026)
__TMUX_TARGET_TAILS__
--- session=bcl2fq_scratch_dra_20260603T011121Z exists=yes
0: bash* (1 panes) [80x24] [layout b25d,80x24,0,0,0] @0 (active)
0: [80x24] [history 140/2000, 49648 bytes] %0 (active)
da-us-west-2d-xxaabb2   ubuntu,ubuntu
da-us-west-2d-dyoa-usw2d-07375  ubuntu,
da-us-west-2d-dyoa-bigboy       ubuntu,
da-us-west-2d-dyoa-smn12-go     ubuntu,
da-us-west-2d-giab-test ubuntu,
da-us-west-2d-ifx-tests ubuntu,
da-us-west-2d-lfg-usw2d ubuntu,
da-us-west-2d-jem-split-test    ubuntu,
da-us-west-2d-jemtest2  ubuntu,
da-us-west-2d-jem-usw2-3        ubuntu,
da-us-west-2d-uswest2d-A        ubuntu,
da-us-west-2d-usw2d-B   ubuntu,
da-us-west-2d-cher-usw2 ubuntu,
da-us-west-2d-tearit-usw2       ubuntu,
da-us-west-2d-gogogo    ubuntu,
da-us-west-2d-josh-test-dev     ubuntu,
da-us-west-2d-agbt-usw2d-primary        ubuntu,
da-us-west-2d-agbt--wrkhrse-usw2        ubuntu,
da-us-west-2d-agbt--12-usw2d    ubuntu,
da-us-west-2d-agbt-12t-usw2d    ubuntu,
da-us-west-2d-day-test-uswest2d ubuntu,daylily-service
da-us-west-2d-day-forge-usw2d   ubuntu,root
da-us-west-2d-agbt-heavy        ubuntu,
da-us-west-2d-daylily-1773059211        ubuntu,root
da-us-west-2d-ifx-go    ubuntu,daylily-service
da-us-west-2d-and-again ubuntu,ubuntu
da-us-west-2d-jemx2     ubuntu,root
da-us-west-2d-y260609-frz       ubuntu
da-us-west-2d-lsbio-fork-260509-124701  ubuntu
da-us-west-2d-fk-260509-use     ubuntu
da-us-west-2d-pilot-mk  ubuntu
da-us-west-2d-pilot-largecluster        ubuntu
da-us-west-2d-may26-d   ubuntu
da-us-west-2d-dra-enabled       ubuntu
da-us-west-2d-XLpilot   ubuntu
da-us-west-2d-XL-pilot  ubuntu
da-us-west-2d-tstVer4-1-1       ubuntu
da-us-west-2d-fork-fixer        ubuntu
da-us-west-2d-tstClu-4-1-1c     ubuntu
da-us-west-2d-splitdra-ref-20260526     ubuntu
da-us-west-2d-jem-bucktst3      ubuntu
da-us-west-2d-blahab44  ubuntu
da-us-west-2d-goodole3  ubuntu
da-us-west-2d-dyec-test ubuntu
da-us-west-2d-dyec5115  ubuntu
da-us-west-2d-dyec5117  ubuntu
da-us-west-2d-dyec0602bcl       ubuntu

you may modify this script to fully block unknown projects, for now this will ta
g with the specified project and proceed.
a log of warnings/errors will be written to ./sbatch_errs.log
setting project=unknown-project
1
             JOBID    PARTITION                     NAME     USER ST       TIME
 NODES NODELIST(REASON)
                 1       bcl2fq    bcl2fq_scratch_to_dra   ubuntu PD       0:00
     1 (None)
(DAY-EC) ubuntu@ip-10-0-0-235:~/daylily-runs/bcl2fq_scratch_to_dra_20260603T0111
21Z$
--- session=dayoa_bcl2fq_scratch_dra_20260603 exists=yes
0: bash* (1 panes) [80x24] [layout b25e,80x24,0,0,1] @1 (active)
0: [80x24] [history 1898/2000, 688324 bytes] %1 (active)
_0009_B23TVLGLT4/fasts_from_bclconvert/lane_reports/L004/SampleSheet.csv false f
alse false 1 8 2 24 8 false true 1000 '{"BarcodeMismatchesIndex1": "0", "Barcode
MismatchesIndex2": "0"}' '{}'  48 /fsx/run_dir_mounts/20260514_LH01106_0009_B23T
VLGLT4/fasts_from_bclconvert/logs/run_bclconvert.L004.log /fsx/run_dir_mounts/20
260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert/lane_fastqs/L004/Reports/fa
stq_list.csv /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bcl
convert/lane_fastqs/L004/Reports/Demultiplex_Stats.csv /fsx/run_dir_mounts/20260
514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert/lane_reports/L004/bclconvert.d
one "" /scratch/dayoa_bclconvert
Submitted job 6 with external jobid '8'.

[Wed Jun  3 03:17:02 2026]
rule run_bclconvert_lane:
    input: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclco
nvert/logs/validated.ok, /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fa
sts_from_bclconvert/normalized.SampleSheet.csv
    output: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclc
onvert/lane_reports/L005/bclconvert.done, /fsx/run_dir_mounts/20260514_LH01106_0
009_B23TVLGLT4/fasts_from_bclconvert/lane_fastqs/L005/Reports/fastq_list.csv, /f
sx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert/lane_fa
stqs/L005/Reports/Demultiplex_Stats.csv, /fsx/run_dir_mounts/20260514_LH01106_00
09_B23TVLGLT4/fasts_from_bclconvert/lane_reports/L005/SampleSheet.csv
    log: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconv
ert/logs/run_bclconvert.L005.log
    jobid: 7
    benchmark: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_b
clconvert/benchmarks/run_bclconvert.L005.bench.tsv
    reason: Missing output files: /fsx/run_dir_mounts/20260514_LH01106_0009_B23T
VLGLT4/fasts_from_bclconvert/lane_fastqs/L005/Reports/fastq_list.csv, /fsx/run_d
ir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert/lane_fastqs/L00
5/Reports/Demultiplex_Stats.csv, /fsx/run_dir_mounts/20260514_LH01106_0009_B23TV
LGLT4/fasts_from_bclconvert/lane_reports/L005/SampleSheet.csv, /fsx/run_dir_moun
ts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert/lane_reports/L005/bclc
onvert.done; Input files updated by another job: /fsx/run_dir_mounts/20260514_LH
01106_0009_B23TVLGLT4/fasts_from_bclconvert/logs/validated.ok, /fsx/run_dir_moun
ts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert/normalized.SampleSheet
.csv
    wildcards: lane=L005
    threads: 48
    resources: mem_mb=300000, mem_mib=286103, disk_mb=1000, disk_mib=954, tmpdir
=<TBD>, threads=48, time=5440, partition=bcl2fq, vcpu=48, distribution=block, ex
clusive=--exclusive, constraint=--constraint=nvme48, exclude=, include=

TMPDIR=/scratch/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/lane_fastqs/L005 /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_f
rom_bclconvert/normalized.SampleSheet.csv 5 /fsx/run_dir_mounts/20260514_LH01106
_0009_B23TVLGLT4/fasts_from_bclconvert/lane_reports/L005/SampleSheet.csv false f
alse false 1 8 2 24 8 false true 1000 '{"BarcodeMismatchesIndex1": "0", "Barcode
MismatchesIndex2": "0"}' '{}'  48 /fsx/run_dir_mounts/20260514_LH01106_0009_B23T
VLGLT4/fasts_from_bclconvert/logs/run_bclconvert.L005.log /fsx/run_dir_mounts/20
260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert/lane_fastqs/L005/Reports/fa
stq_list.csv /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bcl
convert/lane_fastqs/L005/Reports/Demultiplex_Stats.csv /fsx/run_dir_mounts/20260
514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert/lane_reports/L005/bclconvert.d
one "" /scratch/dayoa_bclconvert
Submitted job 7 with external jobid '9'.

--- session=dayoa_bcl_l003_bcl2fq_scratch_20260603 exists=yes
0: bash* (1 panes) [80x24] [layout b25f,80x24,0,0,2] @2 (active)
0: [80x24] [history 581/2000, 198760 bytes] %2 (active)
Activating conda environment: ../../../../resources/environments/conda/ubuntu/ip
-10-0-0-235/9d47d7d0d1fd2da30ac182cf088a614c_
[Wed Jun  3 03:48:47 2026]
Finished job 1.
1 of 4 steps (25%) done
Select jobs to execute...

[Wed Jun  3 03:48:47 2026]
rule run_bclconvert_lane:
    input: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclco
nvert_l003_scratch_test/logs/validated.ok, /fsx/run_dir_mounts/20260514_LH01106_
0009_B23TVLGLT4/fasts_from_bclconvert_l003_scratch_test/normalized.SampleSheet.c
sv
    output: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclc
onvert_l003_scratch_test/lane_reports/L003/bclconvert.done, /fsx/run_dir_mounts/
20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_scratch_test/lane_fa
stqs/L003/Reports/fastq_list.csv, /fsx/run_dir_mounts/20260514_LH01106_0009_B23T
VLGLT4/fasts_from_bclconvert_l003_scratch_test/lane_fastqs/L003/Reports/Demultip
lex_Stats.csv, /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_b
clconvert_l003_scratch_test/lane_reports/L003/SampleSheet.csv
    log: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconv
ert_l003_scratch_test/logs/run_bclconvert.L003.log
    jobid: 3
    benchmark: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_b
clconvert_l003_scratch_test/benchmarks/run_bclconvert.L003.bench.tsv
    reason: Missing output files: /fsx/run_dir_mounts/20260514_LH01106_0009_B23T
VLGLT4/fasts_from_bclconvert_l003_scratch_test/lane_reports/L003/bclconvert.done
, /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l00
3_scratch_test/lane_reports/L003/SampleSheet.csv, /fsx/run_dir_mounts/20260514_L
H01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_scratch_test/lane_fastqs/L003/
Reports/Demultiplex_Stats.csv, /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLG
LT4/fasts_from_bclconvert_l003_scratch_test/lane_fastqs/L003/Reports/fastq_list.
csv; Input files updated by another job: /fsx/run_dir_mounts/20260514_LH01106_00
09_B23TVLGLT4/fasts_from_bclconvert_l003_scratch_test/logs/validated.ok, /fsx/ru
n_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_scratch
_test/normalized.SampleSheet.csv
    wildcards: lane=L003
    threads: 48
    resources: mem_mb=300000, mem_mib=286103, disk_mb=1000, disk_mib=954, tmpdir
=<TBD>, threads=48, time=5440, partition=bcl2fq, vcpu=48, distribution=block, ex
clusive=--exclusive, constraint=, exclude=, include=

TMPDIR=/scratch/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_scratch_test/lane_fastqs/L003 /fsx/run_dir_mounts/20260514_LH01106_0009_
B23TVLGLT4/fasts_from_bclconvert_l003_scratch_test/normalized.SampleSheet.csv 3
/fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_
scratch_test/lane_reports/L003/SampleSheet.csv false false false 1 8 2 24 8 fals
e true 1000 '{"BarcodeMismatchesIndex1": "0", "BarcodeMismatchesIndex2": "0"}' '
{}'  48 /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconve
rt_l003_scratch_test/logs/run_bclconvert.L003.log /fsx/run_dir_mounts/20260514_L
H01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_scratch_test/lane_fastqs/L003/
Reports/fastq_list.csv /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fast
s_from_bclconvert_l003_scratch_test/lane_fastqs/L003/Reports/Demultiplex_Stats.c
sv /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l0
03_scratch_test/lane_reports/L003/bclconvert.done "" /scratch/dayoa_bclconvert
Submitted job 3 with external jobid '10'.

__CONTROLLER_PROCESSES__
  30890   25989 ubuntu   S+   Wed Jun  3 03:16:32 2026 bash bin/day_run produce_bclconvert_fastqs -p -k -j 8 --rerun-triggers mtime --configfile config/bclconvert_scratch_dra.yaml
  31067   30890 ubuntu   S+   Wed Jun  3 03:16:34 2026 bash bin/day_run produce_bclconvert_fastqs -p -k -j 8 --rerun-triggers mtime --configfile config/bclconvert_scratch_dra.yaml
  31068   31067 ubuntu   Sl+  Wed Jun  3 03:16:34 2026 /home/ubuntu/miniconda3/envs/DAYOA/bin/python /home/ubuntu/miniconda3/envs/DAYOA/bin/snakemake --profile=/fsx/analysis_results/dyec0602bcl/bcl2fq_scratch_dra_dayoa_20260603/daylily-omics-analysis/config/day_profiles/slurm produce_bclconvert_fastqs -p -k -j 8 --rerun-triggers mtime --configfile config/bclconvert_scratch_dra.yaml
  31069   31067 ubuntu   S+   Wed Jun  3 03:16:34 2026 bash bin/day_run produce_bclconvert_fastqs -p -k -j 8 --rerun-triggers mtime --configfile config/bclconvert_scratch_dra.yaml
  48541   46045 ubuntu   S+   Wed Jun  3 03:48:39 2026 bash bin/day_run produce_bclconvert_fastqs -p -k -j 1 --rerun-triggers mtime --configfile config/bclconvert_l003_scratch.yaml
  48717   48541 ubuntu   S+   Wed Jun  3 03:48:41 2026 bash bin/day_run produce_bclconvert_fastqs -p -k -j 1 --rerun-triggers mtime --configfile config/bclconvert_l003_scratch.yaml
  48718   48717 ubuntu   Sl+  Wed Jun  3 03:48:41 2026 /home/ubuntu/miniconda3/envs/DAYOA/bin/python /home/ubuntu/miniconda3/envs/DAYOA/bin/snakemake --profile=/fsx/analysis_results/dyec0602bcl/bcl_l003_bcl2fq_scratch_20260603T033830Z/daylily-omics-analysis/config/day_profiles/slurm produce_bclconvert_fastqs -p -k -j 1 --rerun-triggers mtime --configfile config/bclconvert_l003_scratch.yaml
  48719   48717 ubuntu   S+   Wed Jun  3 03:48:41 2026 bash bin/day_run produce_bclconvert_fastqs -p -k -j 1 --rerun-triggers mtime --configfile config/bclconvert_l003_scratch.yaml

