DAY-EC activated.
DAY-EC activated.
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-225/841ac27cc5e7759e4ad9d0f5f4e02ac4_
base                   /home/ubuntu/miniconda3
DAY-EC               * /home/ubuntu/miniconda3/envs/DAY-EC
DAYOA                  /home/ubuntu/miniconda3/envs/DAYOA

Day CLI initialized for project 'dyec5117' 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 build for the current environment.
	                           
	(day-run / dy-r)          - Run a command in the current environment.
	                           <tab> for exposed targets, -<tab> for all command line flags.
	                           
	(day-monitor / dy-m)      - Monitor workflow status (Snakemake, SLURM, logs).
	                           Use --block-and-poll to wait for completion.
	                           
	(day-deactivate / dy-d)   - Deactivate the current environment.
	                           Use 'dy-d reset' to hard reset the environment.
	                           
	                           
	                           
	                           
	. 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/samples.tsv

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



		# 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 statistics



		# 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 calling

		dy-r produce_sentdug_vcf -p -k -j 20 -n        # Ultima SNV calling (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+ONT 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+ONT Modular (use hg38_broad)



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

Requesting profile: slurm
Attempting to deactivate existing environments & re-init with --project dyec5117 .
Remote call detected. Activating conda hack
 > >> >>> 
ACTIVE CONFIG FILES NOT FOUND IN /fsx/analysis_results/ubuntu/bcl25b_l003_shard008_cpu_tuned_odirect_on_20260602T000733Z/daylily-omics-analysis/config/day_profiles/slurm ... copying
Copying template yaml files to active config files /fsx/analysis_results/ubuntu/bcl25b_l003_shard008_cpu_tuned_odirect_on_20260602T000733Z/daylily-omics-analysis/config/day_profiles/slurm
Copying template bash files to active config files /fsx/analysis_results/ubuntu/bcl25b_l003_shard008_cpu_tuned_odirect_on_20260602T000733Z/daylily-omics-analysis/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_Sciences_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 compared 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 _______       
[INFO] Patched /fsx/analysis_results/ubuntu/bcl25b_l003_shard008_cpu_tuned_odirect_on_20260602T000733Z/daylily-omics-analysis/config/day_profiles/slurm/rule_config.yaml bclconvert direct mounted-input mode for 20260514_LH01106_0009_B23TVLGLT4: /fsx/analysis_results/ubuntu/bcl25b_l003_shard008_cpu_tuned_odirect_on_20260602T000733Z/daylily-omics-analysis/config/run_dir_links/20260514_LH01106_0009_B23TVLGLT4
[INFO] DayOA native BCL Convert lane-split rules detected; no DYEC runtime rule patch applied.
Remote call detected. Activating conda hack
Your config files in /fsx/analysis_results/ubuntu/bcl25b_l003_shard008_cpu_tuned_odirect_on_20260602T000733Z/daylily-omics-analysis/config/day_profiles/slurm are newer than the templates. clear 2 go.
Executing: snakemake --profile=/fsx/analysis_results/ubuntu/bcl25b_l003_shard008_cpu_tuned_odirect_on_20260602T000733Z/daylily-omics-analysis/config/day_profiles/slurm produce_bclconvert_fastqs -p -j 384 -k --config run_context_file=config/runs.tsv bootstrap_bclconvert=true bclconvert={"barcode_mismatches_index1":"0","barcode_mismatches_index2":"0","compression_threads":"64","conversion_threads":"4","decompression_threads":"32","fastq_gzip_compression_level":"1","force":"true","merge_lane_fastqs":"false","merge_tile_fastqs":"false","num_unknown_barcodes_reported":"1000","output_legacy_stats":"true","parallel_tiles":"24","partition":"i192mem","sample_sheet_settings":"{}","sample_sheet_settings_by_lane":"{}","shared_thread_odirect_output":"true","threads":"192","tile_compression_threads":"8","tile_conversion_threads":"2","tile_decompression_threads":"8","tile_parallel_tiles":"16","tile_shard_lanes":"L003","tile_shard_level":"8","tile_shard_mem_mb":"180000","tile_shard_threads":"48","tmpdir":"/dev/shm"}
Config file config/global.yaml is extended by additional config specified via the command line.
loading global: /fsx/analysis_results/ubuntu/bcl25b_l003_shard008_cpu_tuned_odirect_on_20260602T000733Z/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/ubuntu/bcl25b_l003_shard008_cpu_tuned_odirect_on_20260602T000733Z/daylily-omics-analysis/config/day_profiles/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): []
A    N   A   L  Y S I S    SAMPLE TABLE DETECTED ::: /fsx/analysis_results/ubuntu/bcl25b_l003_shard008_cpu_tuned_odirect_on_20260602T000733Z/daylily-omics-analysis/config/samples.tsv
A    N   A   L  Y S I S    UNIT TABLE DETECTED ::: /fsx/analysis_results/ubuntu/bcl25b_l003_shard008_cpu_tuned_odirect_on_20260602T000733Z/daylily-omics-analysis/config/units.tsv
Building DAG of jobs...
Using shell: /home/ubuntu/miniconda3/envs/DAY-EC/bin/bash
Provided cluster nodes: 384
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           8             48             48
total                              12              1             48

Select jobs to execute...

[Tue Jun  2 11:15:44 2026]
localrule bclconvert_validate_inputs:
    input: /fsx/analysis_results/ubuntu/bcl25b_l003_shard008_cpu_tuned_odirect_on_20260602T000733Z/daylily-omics-analysis/config/run_dir_links/20260514_LH01106_0009_B23TVLGLT4/SampleSheet.csv, /fsx/analysis_results/ubuntu/bcl25b_l003_shard008_cpu_tuned_odirect_on_20260602T000733Z/daylily-omics-analysis/config/samples.tsv
    output: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/validated.ok, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/normalized.SampleSheet.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tables/samplesheet_rows.tsv
    log: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert_validate_inputs.log
    jobid: 1
    benchmark: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/benchmarks/bclconvert_validate_inputs.bench.tsv
    reason: Missing output files: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/validated.ok, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/normalized.SampleSheet.csv
    resources: mem_mb=3000, mem_mib=2862, disk_mb=1000, disk_mib=954, tmpdir=/dev/shm, threads=1, time=5440, partition=i192,i128,i192mem, vcpu=1, distribution=block, exclusive=, constraint=, exclude=, include=


        set -euo pipefail
        mkdir -p results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tables
        : > results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert_validate_inputs.log
        if [ -z /fsx/analysis_results/ubuntu/bcl25b_l003_shard008_cpu_tuned_odirect_on_20260602T000733Z/daylily-omics-analysis/config/run_dir_links/20260514_LH01106_0009_B23TVLGLT4 ]; then
            echo "bclconvert.run_dir is required" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert_validate_inputs.log
            exit 2
        fi
        if [ ! -d /fsx/analysis_results/ubuntu/bcl25b_l003_shard008_cpu_tuned_odirect_on_20260602T000733Z/daylily-omics-analysis/config/run_dir_links/20260514_LH01106_0009_B23TVLGLT4 ]; then
            echo "bclconvert.run_dir does not exist: /fsx/analysis_results/ubuntu/bcl25b_l003_shard008_cpu_tuned_odirect_on_20260602T000733Z/daylily-omics-analysis/config/run_dir_links/20260514_LH01106_0009_B23TVLGLT4" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert_validate_inputs.log
            exit 2
        fi
        if [ "true" = "false" ]; then
            echo "keep_undetermined_fastqs=false is unsupported for the bclconvert bootstrap path" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert_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 bootstrap workflow" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert_validate_inputs.log
            exit 2
        fi
        python workflow/scripts/parse_bclconvert_samplesheet.py \
          --sample-sheet /fsx/analysis_results/ubuntu/bcl25b_l003_shard008_cpu_tuned_odirect_on_20260602T000733Z/daylily-omics-analysis/config/run_dir_links/20260514_LH01106_0009_B23TVLGLT4/SampleSheet.csv \
          --samples-tsv /fsx/analysis_results/ubuntu/bcl25b_l003_shard008_cpu_tuned_odirect_on_20260602T000733Z/daylily-omics-analysis/config/samples.tsv \
          --normalized-out results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/normalized.SampleSheet.csv \
          --rows-out results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tables/samplesheet_rows.tsv \
          --runtime-version 4.0.3 \
          --sampleproject-subdirectories false \
          --warnings-out results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert_validate_inputs.warnings.log \
          >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert_validate_inputs.log 2>&1
        touch results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/validated.ok
        
Activating conda environment: ../../../../resources/environments/conda/ubuntu/ip-10-0-0-225/841ac27cc5e7759e4ad9d0f5f4e02ac4_
[Tue Jun  2 11:15:45 2026]
Finished job 1.
1 of 12 steps (8%) done
Select jobs to execute...

[Tue Jun  2 11:15:45 2026]
rule run_bclconvert_tile_shard:
    input: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/validated.ok, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/normalized.SampleSheet.csv
    output: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_reports/L003/0003_tiles0197-0294/bclconvert.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_fastqs/L003/0003_tiles0197-0294/Reports/fastq_list.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_fastqs/L003/0003_tiles0197-0294/Reports/Demultiplex_Stats.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_reports/L003/0003_tiles0197-0294/SampleSheet.csv
    log: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.L003.0003_tiles0197-0294.log
    jobid: 6
    benchmark: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/benchmarks/run_bclconvert.L003.0003_tiles0197-0294.bench.tsv
    reason: Missing output files: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_fastqs/L003/0003_tiles0197-0294/Reports/Demultiplex_Stats.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_reports/L003/0003_tiles0197-0294/bclconvert.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_fastqs/L003/0003_tiles0197-0294/Reports/fastq_list.csv; Input files updated by another job: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/validated.ok, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/normalized.SampleSheet.csv
    wildcards: lane=L003, shard=0003_tiles0197-0294
    threads: 48
    resources: mem_mb=180000, mem_mib=171662, disk_mb=1000, disk_mib=954, tmpdir=<TBD>, threads=48, time=5440, partition=i192mem, vcpu=48, distribution=block, exclusive=, constraint=, exclude=, include=

TMPDIR=/dev/shm bash workflow/scripts/run_bclconvert_lane.sh docker://nfcore/bclconvert:4.0.3 /fsx/analysis_results/ubuntu/bcl25b_l003_shard008_cpu_tuned_odirect_on_20260602T000733Z/daylily-omics-analysis/config/run_dir_links/20260514_LH01106_0009_B23TVLGLT4 results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_fastqs/L003/0003_tiles0197-0294 results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/normalized.SampleSheet.csv 3 results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_reports/L003/0003_tiles0197-0294/SampleSheet.csv false false false 1 16 2 8 8 true true 1000 '{"BarcodeMismatchesIndex1": "0", "BarcodeMismatchesIndex2": "0"}' '{}' -f 48 results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.L003.0003_tiles0197-0294.log results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_fastqs/L003/0003_tiles0197-0294/Reports/fastq_list.csv results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_fastqs/L003/0003_tiles0197-0294/Reports/Demultiplex_Stats.csv results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_reports/L003/0003_tiles0197-0294/bclconvert.done s_3_1301+s_3_1302+s_3_1303+s_3_1304+s_3_1305+s_3_1306+s_3_1307+s_3_1308+s_3_1309+s_3_1310+s_3_1311+s_3_1312+s_3_1313+s_3_1314+s_3_1315+s_3_1316+s_3_1317+s_3_1318+s_3_1319+s_3_1320+s_3_1321+s_3_1322+s_3_1323+s_3_1324+s_3_1325+s_3_1326+s_3_1327+s_3_1328+s_3_1329+s_3_1330+s_3_1331+s_3_1332+s_3_1333+s_3_1334+s_3_1335+s_3_1336+s_3_1337+s_3_1338+s_3_1339+s_3_1340+s_3_1341+s_3_1342+s_3_1343+s_3_1344+s_3_1345+s_3_1346+s_3_1347+s_3_1348+s_3_1349+s_3_1350+s_3_1351+s_3_1352+s_3_1353+s_3_1354+s_3_1355+s_3_1356+s_3_1357+s_3_1358+s_3_1359+s_3_1360+s_3_1361+s_3_1362+s_3_1363+s_3_1364+s_3_1365+s_3_1366+s_3_1367+s_3_1368+s_3_1369+s_3_1370+s_3_1371+s_3_1372+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_1381+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
Submitted job 6 with external jobid '80'.

[Tue Jun  2 11:15:45 2026]
rule run_bclconvert_tile_shard:
    input: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/validated.ok, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/normalized.SampleSheet.csv
    output: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_reports/L003/0005_tiles0393-0490/bclconvert.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_fastqs/L003/0005_tiles0393-0490/Reports/fastq_list.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_fastqs/L003/0005_tiles0393-0490/Reports/Demultiplex_Stats.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_reports/L003/0005_tiles0393-0490/SampleSheet.csv
    log: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.L003.0005_tiles0393-0490.log
    jobid: 8
    benchmark: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/benchmarks/run_bclconvert.L003.0005_tiles0393-0490.bench.tsv
    reason: Missing output files: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_fastqs/L003/0005_tiles0393-0490/Reports/fastq_list.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_reports/L003/0005_tiles0393-0490/bclconvert.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_fastqs/L003/0005_tiles0393-0490/Reports/Demultiplex_Stats.csv; Input files updated by another job: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/validated.ok, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/normalized.SampleSheet.csv
    wildcards: lane=L003, shard=0005_tiles0393-0490
    threads: 48
    resources: mem_mb=180000, mem_mib=171662, disk_mb=1000, disk_mib=954, tmpdir=<TBD>, threads=48, time=5440, partition=i192mem, vcpu=48, distribution=block, exclusive=, constraint=, exclude=, include=

TMPDIR=/dev/shm bash workflow/scripts/run_bclconvert_lane.sh docker://nfcore/bclconvert:4.0.3 /fsx/analysis_results/ubuntu/bcl25b_l003_shard008_cpu_tuned_odirect_on_20260602T000733Z/daylily-omics-analysis/config/run_dir_links/20260514_LH01106_0009_B23TVLGLT4 results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_fastqs/L003/0005_tiles0393-0490 results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/normalized.SampleSheet.csv 3 results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_reports/L003/0005_tiles0393-0490/SampleSheet.csv false false false 1 16 2 8 8 true true 1000 '{"BarcodeMismatchesIndex1": "0", "BarcodeMismatchesIndex2": "0"}' '{}' -f 48 results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.L003.0005_tiles0393-0490.log results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_fastqs/L003/0005_tiles0393-0490/Reports/fastq_list.csv results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_fastqs/L003/0005_tiles0393-0490/Reports/Demultiplex_Stats.csv results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_reports/L003/0005_tiles0393-0490/bclconvert.done s_3_2101+s_3_2102+s_3_2103+s_3_2104+s_3_2105+s_3_2106+s_3_2107+s_3_2108+s_3_2109+s_3_2110+s_3_2111+s_3_2112+s_3_2113+s_3_2114+s_3_2115+s_3_2116+s_3_2117+s_3_2118+s_3_2119+s_3_2120+s_3_2121+s_3_2122+s_3_2123+s_3_2124+s_3_2125+s_3_2126+s_3_2127+s_3_2128+s_3_2129+s_3_2130+s_3_2131+s_3_2132+s_3_2133+s_3_2134+s_3_2135+s_3_2136+s_3_2137+s_3_2138+s_3_2139+s_3_2140+s_3_2141+s_3_2142+s_3_2143+s_3_2144+s_3_2145+s_3_2146+s_3_2147+s_3_2148+s_3_2149+s_3_2150+s_3_2151+s_3_2152+s_3_2153+s_3_2154+s_3_2155+s_3_2156+s_3_2157+s_3_2158+s_3_2159+s_3_2160+s_3_2161+s_3_2162+s_3_2163+s_3_2164+s_3_2165+s_3_2166+s_3_2167+s_3_2168+s_3_2169+s_3_2170+s_3_2171+s_3_2172+s_3_2173+s_3_2174+s_3_2175+s_3_2176+s_3_2177+s_3_2178+s_3_2179+s_3_2180+s_3_2181+s_3_2182+s_3_2183+s_3_2184+s_3_2185+s_3_2186+s_3_2187+s_3_2188+s_3_2189+s_3_2190+s_3_2191+s_3_2192+s_3_2193+s_3_2194+s_3_2195+s_3_2196+s_3_2197+s_3_2198
Submitted job 8 with external jobid '81'.

[Tue Jun  2 11:15:45 2026]
rule run_bclconvert_tile_shard:
    input: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/validated.ok, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/normalized.SampleSheet.csv
    output: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_reports/L003/0002_tiles0099-0196/bclconvert.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_fastqs/L003/0002_tiles0099-0196/Reports/fastq_list.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_fastqs/L003/0002_tiles0099-0196/Reports/Demultiplex_Stats.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_reports/L003/0002_tiles0099-0196/SampleSheet.csv
    log: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.L003.0002_tiles0099-0196.log
    jobid: 5
    benchmark: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/benchmarks/run_bclconvert.L003.0002_tiles0099-0196.bench.tsv
    reason: Missing output files: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_reports/L003/0002_tiles0099-0196/bclconvert.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_fastqs/L003/0002_tiles0099-0196/Reports/fastq_list.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_fastqs/L003/0002_tiles0099-0196/Reports/Demultiplex_Stats.csv; Input files updated by another job: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/validated.ok, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/normalized.SampleSheet.csv
    wildcards: lane=L003, shard=0002_tiles0099-0196
    threads: 48
    resources: mem_mb=180000, mem_mib=171662, disk_mb=1000, disk_mib=954, tmpdir=<TBD>, threads=48, time=5440, partition=i192mem, vcpu=48, distribution=block, exclusive=, constraint=, exclude=, include=

TMPDIR=/dev/shm bash workflow/scripts/run_bclconvert_lane.sh docker://nfcore/bclconvert:4.0.3 /fsx/analysis_results/ubuntu/bcl25b_l003_shard008_cpu_tuned_odirect_on_20260602T000733Z/daylily-omics-analysis/config/run_dir_links/20260514_LH01106_0009_B23TVLGLT4 results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_fastqs/L003/0002_tiles0099-0196 results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/normalized.SampleSheet.csv 3 results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_reports/L003/0002_tiles0099-0196/SampleSheet.csv false false false 1 16 2 8 8 true true 1000 '{"BarcodeMismatchesIndex1": "0", "BarcodeMismatchesIndex2": "0"}' '{}' -f 48 results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.L003.0002_tiles0099-0196.log results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_fastqs/L003/0002_tiles0099-0196/Reports/fastq_list.csv results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_fastqs/L003/0002_tiles0099-0196/Reports/Demultiplex_Stats.csv results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_reports/L003/0002_tiles0099-0196/bclconvert.done s_3_1201+s_3_1202+s_3_1203+s_3_1204+s_3_1205+s_3_1206+s_3_1207+s_3_1208+s_3_1209+s_3_1210+s_3_1211+s_3_1212+s_3_1213+s_3_1214+s_3_1215+s_3_1216+s_3_1217+s_3_1218+s_3_1219+s_3_1220+s_3_1221+s_3_1222+s_3_1223+s_3_1224+s_3_1225+s_3_1226+s_3_1227+s_3_1228+s_3_1229+s_3_1230+s_3_1231+s_3_1232+s_3_1233+s_3_1234+s_3_1235+s_3_1236+s_3_1237+s_3_1238+s_3_1239+s_3_1240+s_3_1241+s_3_1242+s_3_1243+s_3_1244+s_3_1245+s_3_1246+s_3_1247+s_3_1248--output truncated--
