command_id=11078f40-5845-42c7-a89c-a1bf0867630d
DAY-EC activated.
DAY-EC activated.
__DATE__=2026-06-03T06:24:48+00:00
cd /fsx/analysis_results/dyec0602bcl/bcl_l003_6shard_i192bigmem_devshm_argfix_20
260603T0620Z/daylily-omics-analysis
source dyoainit
dy-a slurm hg38
DAY-EC activated.
(DAY-EC) ubuntu@ip-10-0-0-235:~$ cd /fsx/analysis_results/dyec0602bcl/bcl_l003_6
shard_i192bigmem_devshm_argfix_20260603T0620Z/daylily-omics-analysis
(DAY-EC) ubuntu@ip-10-0-0-235:/fsx/analysis_results/dyec0602bcl/bcl_l003_6shard_
i192bigmem_devshm_argfix_20260603T0620Z/daylily-omics-analysis$ source dyoainit
Notice: --project not set. Using default project name: dyec0602bcl
Notice: Cluster config sets aws-parallelcluster-enforce-budget=skip; skipping pr
oject validation.
Project: dyec0602bcl
Skip Project Check: true
Skipping project validation as --skip-project-check was passed.

________________________________________________________
AWS Budget lookup skipped for project 'dyec0602bcl' in region 'us-west-2'.
  Total: NA
  Used: NA
  Percent Used: NA
________________________________________________________
WARNING: SENTIEON_LICENSE was not configured with a valid file; auto assigning a
 detected Sentieon license: /fsx/references/runtime_assets/cached_envs/Life_Scie
nces_Manufacturing_Corporation_eval.lic

# conda environments:
#
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-235/9d
47d7d0d1fd2da30ac182cf088a614c_
base                   /home/ubuntu/miniconda3
DAY-EC               * /home/ubuntu/miniconda3/envs/DAY-EC
DAYOA                  /home/ubuntu/miniconda3/envs/DAYOA

Day CLI initialized for project 'dyec0602bcl' in region 'us-west-2'.
The Daylily CLI is now available.
Available commands (tab completion is enabled for all):

        (day-activate / dy-a) [slurm|local] ([hg38|hg38_broad|b37])- Activate a
Slurm or local environment.

        {day-set-genome-build / dy-g) [b37|hg38|hg38_broad] - Set the genome bui
ld for the current environment.

        (day-run / dy-r)          - Run a command in the current environment.
                                   <tab> for exposed targets, -<tab> for all com
mand line flags.

        (day-monitor / dy-m)      - Monitor workflow status (Snakemake, SLURM, l
ogs).
                                   Use --block-and-poll to wait for completion.

        (day-deactivate / dy-d)   - Deactivate the current environment.
                                   Use 'dy-d reset' to hard reset the environmen
t.




        . To Stage Sample Data, see daylily-ephemeral-cluster docs for running ~
/projects/daylily-ephemeral-cluster/bin/daylily-stage-analysis-samples-headnode
          ... which once run, you will copy the samples.tsv and units.tsv files
to config/ in this directory.

        (example): ACTIVATE AN ANALYSIS ENV





                dy-a slurm hg38 # or hg38_broad or b37

        (example): RUN ANALYSES

                cp .test_data/data/0.01xwgs_HG002_hg38.samples.tsv config/sample
s.tsv

                cp .test_data/data/0.01xwgs_HG002_hg38.units.tsv config/units.ts
v



                # Use target names directly (tab-complete available):

                dy-r produce_snv_concordances -p -k -j 20 -n   # Illumina short-
read SNV concordance

                dy-r produce_alignstats -p -k -j 20 -n         # Alignment stati
stics



                # Platform-specific targets:

                dy-r produce_sentdont_vcf -p -k -j 20 -n       # ONT SNV calling

                dy-r produce_sentdpb_vcf -p -k -j 20 -n        # PacBio SNV call
ing

                dy-r produce_sentdug_vcf -p -k -j 20 -n        # Ultima SNV call
ing (use hg38_broad)



                # Hybrid workflow targets:

                dy-r produce_sentdhio_vcf -p -k -j 20 -n       # Hybrid Illumina
+ONT CLI

                dy-r produce_sentdhuo_vcf -p -k -j 20 -n       # Hybrid Ultima+O
NT CLI (use hg38_broad)

                dy-r produce_sentdhiom_vcf -p -k -j 20 -n      # Hybrid Illumina
+ONT Modular

                dy-r produce_sentdhuom_vcf -p -k -j 20 -n      # Hybrid Ultima+O
NT Modular (use hg38_broad)



                # Remove -n to execute (not dry-run)

(DAYOA) ubuntu@ip-10-0-0-235:/fsx/analysis_results/dyec0602bcl/bcl_l003_6shard_i
192bigmem_devshm_argfix_20260603T0620Z/daylily-omics-analysis$ dy-a slurm hg38
Requesting profile: slurm
Attempting to deactivate existing environments & re-init with --project dyec0602
bcl .
 > >> >>>
ACTIVE CONFIG FILES NOT FOUND IN /fsx/analysis_results/dyec0602bcl/bcl_l003_6sha
rd_i192bigmem_devshm_argfix_20260603T0620Z/daylily-omics-analysis/config/day_pro
files/slurm ... copying
Copying template yaml files to active config files /fsx/analysis_results/dyec060
2bcl/bcl_l003_6shard_i192bigmem_devshm_argfix_20260603T0620Z/daylily-omics-analy
sis/config/day_profiles/slurm
Copying template bash files to active config files /fsx/analysis_results/dyec060
2bcl/bcl_l003_6shard_i192bigmem_devshm_argfix_20260603T0620Z/daylily-omics-analy
sis/config/day_profiles/slurm
yq is already installed.
WARNING: sentieon lic file /fsx/references/runtime_assets/cached_envs/x.lic not
found.
WARNING: SENTIEON_LICENSE was not configured with a valid file; auto assigning a
 detected Sentieon license: /fsx/references/runtime_assets/cached_envs/Life_Scie
nces_Manufacturing_Corporation_eval.lic

!!!!
!!!!
    WARNING: gittag:null not found touched in  ~/.config/daylily/null
     This might be fine if you have cloned a more recent release of daylily comp
ared to the tagged version used to create this ephemeral cluster.
     ... however, this is not expected. If you are running an ephemeral cluster
headnode for days+, this is not the intended use of daylily, a fresh build might
 be called for.
     This is checked by testing if ~/.config/daylily/null exists .
!!!!
 > >> >>>   genome build set to ::: hg38
       _______ GREAT SUCCESS _______
[Dslu](DAYOA) cd /fsx/analysis_results/dyec0602bcl/bcl_l003_6shard_i192bigmem_de
vshm_argfix_20260603T0620Z/daylily-omics-analysis
[Dslu](DAYOA) source dyoainit
Notice: Cluster config sets aws-parallelcluster-enforce-budget=skip; skipping pr
oject validation.
Project: dyec0602bcl
Skip Project Check: true
Skipping project validation as --skip-project-check was passed.

________________________________________________________
AWS Budget lookup skipped for project 'dyec0602bcl' in region 'us-west-2'.
  Total: NA
  Used: NA
  Percent Used: NA
________________________________________________________
Using explicit SENTIEON_LICENSE: /fsx/references/runtime_assets/cached_envs/Life
_Sciences_Manufacturing_Corporation_eval.lic

# conda environments:
#
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-235/9d
47d7d0d1fd2da30ac182cf088a614c_
base                   /home/ubuntu/miniconda3
DAY-EC                 /home/ubuntu/miniconda3/envs/DAY-EC
DAYOA                * /home/ubuntu/miniconda3/envs/DAYOA

dy-a slurm hg38
Day CLI initialized for project 'dyec0602bcl' in region 'us-west-2'.
The Daylily CLI is now available.
Available commands (tab completion is enabled for all):

        (day-activate / dy-a) [slurm|local] ([hg38|hg38_broad|b37])- Activate a
Slurm or local environment.

        {day-set-genome-build / dy-g) [b37|hg38|hg38_broad] - Set the genome bui
ld for the current environment.

        (day-run / dy-r)          - Run a command in the current environment.
                                   <tab> for exposed targets, -<tab> for all com
mand line flags.

        (day-monitor / dy-m)      - Monitor workflow status (Snakemake, SLURM, l
ogs).
                                   Use --block-and-poll to wait for completion.

        (day-deactivate / dy-d)   - Deactivate the current environment.
                                   Use 'dy-d reset' to hard reset the environmen
t.




        . To Stage Sample Data, see daylily-ephemeral-cluster docs for running ~
/projects/daylily-ephemeral-cluster/bin/daylily-stage-analysis-samples-headnode
          ... which once run, you will copy the samples.tsv and units.tsv files
to config/ in this directory.

        (example): ACTIVATE AN ANALYSIS ENV





                dy-a slurm hg38 # or hg38_broad or b37

        (example): RUN ANALYSES

                cp .test_data/data/0.01xwgs_HG002_hg38.samples.tsv config/sample
s.tsv

                cp .test_data/data/0.01xwgs_HG002_hg38.units.tsv config/units.ts
v



                # Use target names directly (tab-complete available):

                dy-r produce_snv_concordances -p -k -j 20 -n   # Illumina short-
read SNV concordance

                dy-r produce_alignstats -p -k -j 20 -n         # Alignment stati
stics



                # Platform-specific targets:

                dy-r produce_sentdont_vcf -p -k -j 20 -n       # ONT SNV calling

                dy-r produce_sentdpb_vcf -p -k -j 20 -n        # PacBio SNV call
ing

                dy-r produce_sentdug_vcf -p -k -j 20 -n        # Ultima SNV call
ing (use hg38_broad)



                # Hybrid workflow targets:

                dy-r produce_sentdhio_vcf -p -k -j 20 -n       # Hybrid Illumina
+ONT CLI

                dy-r produce_sentdhuo_vcf -p -k -j 20 -n       # Hybrid Ultima+O
NT CLI (use hg38_broad)

                dy-r produce_sentdhiom_vcf -p -k -j 20 -n      # Hybrid Illumina
+ONT Modular

                dy-r produce_sentdhuom_vcf -p -k -j 20 -n      # Hybrid Ultima+O
NT Modular (use hg38_broad)



                # Remove -n to execute (not dry-run)

(DAYOA) [Dslu]dy-a slurm hg38
Requesting profile: slurm
dy-r produce_bclconvert_fastqs -p -k -j 10 --rerun-triggers mtime --configfile c
onfig/bclconvert_l003_6shard_i192bigmem_devshm_argfix.yaml -n; printf "__DRYRUN_
ARGFIX_EXIT__=%s\n" "$?"
Attempting to deactivate existing environments & re-init with --project dyec0602
bcl .
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.
yq is already installed.
WARNING: sentieon lic file /fsx/references/runtime_assets/cached_envs/x.lic not
found.
WARNING: SENTIEON_LICENSE was not configured with a valid file; auto assigning a
 detected Sentieon license: /fsx/references/runtime_assets/cached_envs/Life_Scie
nces_Manufacturing_Corporation_eval.lic

!!!!
!!!!
    WARNING: gittag:null not found touched in  ~/.config/daylily/null
     This might be fine if you have cloned a more recent release of daylily comp
ared to the tagged version used to create this ephemeral cluster.
     ... however, this is not expected. If you are running an ephemeral cluster
headnode for days+, this is not the intended use of daylily, a fresh build might
 be called for.
     This is checked by testing if ~/.config/daylily/null exists .
!!!!
 > >> >>>   genome build set to ::: hg38
       _______ GREAT SUCCESS _______
[Dslu](DAYOA) dy-r produce_bclconvert_fastqs -p -k -j 10 --rerun-triggers mtime
--configfile config/bclconvert_l003_6shard_i192bigmem_devshm_argfix.yaml -n; pri
ntf "__DRYRUN_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 produce_bclconvert_fastqs -p -k -j 10 --rerun-triggers mtime --configf
ile config/bclconvert_l003_6shard_i192bigmem_devshm_argfix.yaml -n
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): []
     _____ DEFAULT samples.tsv copied to /fsx/analysis_results/dyec0602bcl/bcl_l
003_6shard_i192bigmem_devshm_argfix_20260603T0620Z/daylily-omics-analysis/config
/samples.tsv
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...
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           6            192            192
total                              10              1            192


[Wed Jun  3 06:23:55 2026]
localrule bclconvert_validate_inputs:
    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
    jobid: 1
    benchmark: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_b
clconvert_l003_6shard_i192bigmem_devshm_argfix_20260603T0620Z/benchmarks/bclconv
ert_validate_inputs.bench.tsv
    reason: Missing output files: /fsx/run_dir_mounts/20260514_LH01106_0009_B23T
VLGLT4/fasts_from_bclconvert_l003_6shard_i192bigmem_devshm_argfix_20260603T0620Z
/logs/validated.ok, /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_f
rom_bclconvert_l003_6shard_i192bigmem_devshm_argfix_20260603T0620Z/normalized.Sa
mpleSheet.csv
    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_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


[Wed Jun  3 06:23:55 2026]
rule run_bclconvert_tile_shard:
    input: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclco
nvert_l003_6shard_i192bigmem_devshm_argfix_20260603T0620Z/logs/validated.ok, /fs
x/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6sh
ard_i192bigmem_devshm_argfix_20260603T0620Z/normalized.SampleSheet.csv
    output: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclc
onvert_l003_6shard_i192bigmem_devshm_argfix_20260603T0620Z/tile_reports/L003/000
3_tiles0263-0393/bclconvert.done, /fsx/run_dir_mounts/20260514_LH01106_0009_B23T
VLGLT4/fasts_from_bclconvert_l003_6shard_i192bigmem_devshm_argfix_20260603T0620Z
/tile_fastqs/L003/0003_tiles0263-0393/Reports/fastq_list.csv, /fsx/run_dir_mount
s/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shard_i192bigmem_
devshm_argfix_20260603T0620Z/tile_fastqs/L003/0003_tiles0263-0393/Reports/Demult
iplex_Stats.csv, /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from
_bclconvert_l003_6shard_i192bigmem_devshm_argfix_20260603T0620Z/tile_reports/L00
3/0003_tiles0263-0393/SampleSheet.csv
    log: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconv
ert_l003_6shard_i192bigmem_devshm_argfix_20260603T0620Z/logs/run_bclconvert.L003
.0003_tiles0263-0393.log
    jobid: 6
    benchmark: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_b
clconvert_l003_6shard_i192bigmem_devshm_argfix_20260603T0620Z/benchmarks/run_bcl
convert.L003.0003_tiles0263-0393.bench.tsv
    reason: Missing output files: /fsx/run_dir_mounts/20260514_LH01106_0009_B23T
VLGLT4/fasts_from_bclconvert_l003_6shard_i192bigmem_devshm_argfix_20260603T0620Z
/tile_fastqs/L003/0003_tiles0263-0393/Reports/fastq_list.csv, /fsx/run_dir_mount
s/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shard_i192bigmem_
devshm_argfix_20260603T0620Z/tile_fastqs/L003/0003_tiles0263-0393/Reports/Demult
iplex_Stats.csv, /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from
_bclconvert_l003_6shard_i192bigmem_devshm_argfix_20260603T0620Z/tile_reports/L00
3/0003_tiles0263-0393/bclconvert.done; Input files updated by another job: /fsx/
run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shar
d_i192bigmem_devshm_argfix_20260603T0620Z/logs/validated.ok, /fsx/run_dir_mounts
/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shard_i192bigmem_d
evshm_argfix_20260603T0620Z/normalized.SampleSheet.csv
    wildcards: lane=L003, shard=0003_tiles0263-0393
    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_6shard_i192bigmem_devshm_argfix_20260603T0620Z/tile_fastqs/L003/0003_til
es0263-0393 /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclc
onvert_l003_6shard_i192bigmem_devshm_argfix_20260603T0620Z/normalized.SampleShee
t.csv 3 /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconve
rt_l003_6shard_i192bigmem_devshm_argfix_20260603T0620Z/tile_reports/L003/0003_ti
les0263-0393/SampleSheet.csv false false false 1 24 4 64 32 false true 1000 '{"B
arcodeMismatchesIndex1": "0", "BarcodeMismatchesIndex2": "0"}' '{}' __dayoa_no_f
orce__ 192 /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclco
nvert_l003_6shard_i192bigmem_devshm_argfix_20260603T0620Z/logs/run_bclconvert.L0
03.0003_tiles0263-0393.log /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/
fasts_from_bclconvert_l003_6shard_i192bigmem_devshm_argfix_20260603T0620Z/tile_f
astqs/L003/0003_tiles0263-0393/Reports/fastq_list.csv /fsx/run_dir_mounts/202605
14_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shard_i192bigmem_devshm_a
rgfix_20260603T0620Z/tile_fastqs/L003/0003_tiles0263-0393/Reports/Demultiplex_St
ats.csv /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconve
rt_l003_6shard_i192bigmem_devshm_argfix_20260603T0620Z/tile_reports/L003/0003_ti
les0263-0393/bclconvert.done s_3_1367+s_3_1368+s_3_1369+s_3_1370+s_3_1371+s_3_13
72+s_3_1373+s_3_1374+s_3_1375+s_3_1376+s_3_1377+s_3_1378+s_3_1379+s_3_1380+s_3_1
381+s_3_1382+s_3_1383+s_3_1384+s_3_1385+s_3_1386+s_3_1387+s_3_1388+s_3_1389+s_3_
1390+s_3_1391+s_3_1392+s_3_1393+s_3_1394+s_3_1395+s_3_1396+s_3_1397+s_3_1398+s_3
_1401+s_3_1402+s_3_1403+s_3_1404+s_3_1405+s_3_1406+s_3_1407+s_3_1408+s_3_1409+s_
3_1410+s_3_1411+s_3_1412+s_3_1413+s_3_1414+s_3_1415+s_3_1416+s_3_1417+s_3_1418+s
_3_1419+s_3_1420+s_3_1421+s_3_1422+s_3_1423+s_3_1424+s_3_1425+s_3_1426+s_3_1427+
s_3_1428+s_3_1429+s_3_1430+s_3_1431+s_3_1432+s_3_1433+s_3_1434+s_3_1435+s_3_1436
+s_3_1437+s_3_1438+s_3_1439+s_3_1440+s_3_1441+s_3_1442+s_3_1443+s_3_1444+s_3_144
5+s_3_1446+s_3_1447+s_3_1448+s_3_1449+s_3_1450+s_3_1451+s_3_1452+s_3_1453+s_3_14
54+s_3_1455+s_3_1456+s_3_1457+s_3_1458+s_3_1459+s_3_1460+s_3_1461+s_3_1462+s_3_1
463+s_3_1464+s_3_1465+s_3_1466+s_3_1467+s_3_1468+s_3_1469+s_3_1470+s_3_1471+s_3_
1472+s_3_1473+s_3_1474+s_3_1475+s_3_1476--output truncated--
