command_id=108db8f6-6a56-4110-98b1-81ca1d1b09df
DAY-EC activated.
DAY-EC activated.
__DATE__=2026-06-03T06:16:37+00:00
__SESSION__=dayoa_bcl_l003_6shard_i192bigmem_devshm_20260603
0: bash* (1 panes) [80x24] [layout b260,80x24,0,0,3] @3 (active)
0: [80x24] [history 1923/2000, 749304 bytes] %3 (active)
__PANE_TAIL_BEFORE__
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_1454+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_1463+
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+s_3_1477+s_3_1478+s_3_1479+s_3_1480+s_3_148
1+s_3_1482+s_3_1483+s_3_1484+s_3_1485+s_3_1486+s_3_1487+s_3_1488+s_3_1489+s_3_14
90+s_3_1491+s_3_1492+s_3_1493+s_3_1494+s_3_1495+s_3_1496+s_3_1497+s_3_1498+s_3_2
101 /dev/shm/dayoa_bclconvert 650000000000
        (one of the commands exited with non-zero exit code; note that snakemake
 uses bash strict mode!)
    cluster_jobid: 21

Error executing rule run_bclconvert_tile_shard on cluster (jobid: 6, external: 2
1, jobscript: /fsx/analysis_results/dyec0602bcl/bcl_l003_6shard_i192bigmem_devsh
m_20260603T041747Z/daylily-omics-analysis/.snakemake/tmp.1k8yes_m/snakejob.run_b
clconvert_tile_shard.6.sh). For error details see the cluster log and the log fi
les of the involved rule(s).
[Wed Jun  3 04:37:38 2026]
Error in rule run_bclconvert_tile_shard:
    jobid: 8
    input: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclco
nvert_l003_6shard_i192bigmem_devshm/logs/validated.ok, /fsx/run_dir_mounts/20260
514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shard_i192bigmem_devshm/
normalized.SampleSheet.csv
    output: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclc
onvert_l003_6shard_i192bigmem_devshm/tile_reports/L003/0005_tiles0525-0654/bclco
nvert.done, /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclc
onvert_l003_6shard_i192bigmem_devshm/tile_fastqs/L003/0005_tiles0525-0654/Report
s/fastq_list.csv, /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_fro
m_bclconvert_l003_6shard_i192bigmem_devshm/tile_fastqs/L003/0005_tiles0525-0654/
Reports/Demultiplex_Stats.csv, /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLG
LT4/fasts_from_bclconvert_l003_6shard_i192bigmem_devshm/tile_reports/L003/0005_t
iles0525-0654/SampleSheet.csv
    log: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconv
ert_l003_6shard_i192bigmem_devshm/logs/run_bclconvert.L003.0005_tiles0525-0654.l
og (check log file(s) for error details)
    shell:
        TMPDIR=/dev/shm/dayoa_bclconvert_tmp bash workflow/scripts/run_bclconver
t_lane.sh docker://nfcore/bclconvert:4.0.3 /fsx/run_dir_mounts/20260514_LH01106_
0009_B23TVLGLT4 /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_
bclconvert_l003_6shard_i192bigmem_devshm/tile_fastqs/L003/0005_tiles0525-0654 /f
sx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6s
hard_i192bigmem_devshm/normalized.SampleSheet.csv 3 /fsx/run_dir_mounts/20260514
_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_6shard_i192bigmem_devshm/til
e_reports/L003/0005_tiles0525-0654/SampleSheet.csv false false false 1 24 4 64 3
2 false true 1000 '{"BarcodeMismatchesIndex1": "0", "BarcodeMismatchesIndex2": "
0"}' '{}'  192 /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_b
clconvert_l003_6shard_i192bigmem_devshm/logs/run_bclconvert.L003.0005_tiles0525-
0654.log /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconv
ert_l003_6shard_i192bigmem_devshm/tile_fastqs/L003/0005_tiles0525-0654/Reports/f
astq_list.csv /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bc
lconvert_l003_6shard_i192bigmem_devshm/tile_fastqs/L003/0005_tiles0525-0654/Repo
rts/Demultiplex_Stats.csv /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/f
asts_from_bclconvert_l003_6shard_i192bigmem_devshm/tile_reports/L003/0005_tiles0
525-0654/bclconvert.done s_3_2235+s_3_2236+s_3_2237+s_3_2238+s_3_2239+s_3_2240+s
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2294+s_3_2295+s_3_2296+s_3_2297+s_3_2298+s_3_2301+s_3_2302+s_3_2303+s_3_2304+s_3
_2305+s_3_2306+s_3_2307+s_3_2308+s_3_2309+s_3_2310+s_3_2311+s_3_2312+s_3_2313+s_
3_2314+s_3_2315+s_3_2316+s_3_2317+s_3_2318+s_3_2319+s_3_2320+s_3_2321+s_3_2322+s
_3_2323+s_3_2324+s_3_2325+s_3_2326+s_3_2327+s_3_2328+s_3_2329+s_3_2330+s_3_2331+
s_3_2332+s_3_2333+s_3_2334+s_3_2335+s_3_2336+s_3_2337+s_3_2338+s_3_2339+s_3_2340
+s_3_2341+s_3_2342+s_3_2343+s_3_2344+s_3_2345+s_3_2346+s_3_2347+s_3_2348+s_3_234
9+s_3_2350+s_3_2351+s_3_2352+s_3_2353+s_3_2354+s_3_2355+s_3_2356+s_3_2357+s_3_23
58+s_3_2359+s_3_2360+s_3_2361+s_3_2362+s_3_2363+s_3_2364+s_3_2365+s_3_2366 /dev/
shm/dayoa_bclconvert 650000000000
        (one of the commands exited with non-zero exit code; note that snakemake
 uses bash strict mode!)
    cluster_jobid: 22

Error executing rule run_bclconvert_tile_shard on cluster (jobid: 8, external: 2
2, jobscript: /fsx/analysis_results/dyec0602bcl/bcl_l003_6shard_i192bigmem_devsh
m_20260603T041747Z/daylily-omics-analysis/.snakemake/tmp.1k8yes_m/snakejob.run_b
clconvert_tile_shard.8.sh). For error details see the cluster log and the log fi
les of the involved rule(s).
Exiting because a job execution failed. Look above for error message

        Womp Womp.  something went awry----
RETURN CODE: 1
__LIVE_EXIT__=1
[Dslu](DAYOA)
__SEND_SETUP__
__PANE_TAIL_AFTER_SETUP_SEND__
________________________________________________________
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


