DAY-EC activated.
DAY-EC activated.
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+s_3_1249+s_3_1250+s_3_1251+s_3_1252+s_3_1253+s_3_1254+s_3_1255+s_3_1256+s_3_1257+s_3_1258+s_3_1259+s_3_1260+s_3_1261+s_3_1262+s_3_1263+s_3_1264+s_3_1265+s_3_1266+s_3_1267+s_3_1268+s_3_1269+s_3_1270+s_3_1271+s_3_1272+s_3_1273+s_3_1274+s_3_1275+s_3_1276+s_3_1277+s_3_1278+s_3_1279+s_3_1280+s_3_1281+s_3_1282+s_3_1283+s_3_1284+s_3_1285+s_3_1286+s_3_1287+s_3_1288+s_3_1289+s_3_1290+s_3_1291+s_3_1292+s_3_1293+s_3_1294+s_3_1295+s_3_1296+s_3_1297+s_3_1298
Submitted job 5 with external jobid '82'.

[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/L003/0007_tiles0589-0686/bclconvert.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_fastqs/L003/0007_tiles0589-0686/Reports/fastq_list.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_fastqs/L003/0007_tiles0589-0686/Reports/Demultiplex_Stats.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_reports/L003/0007_tiles0589-0686/SampleSheet.csv
    log: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.L003.0007_tiles0589-0686.log
    jobid: 10
    benchmark: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/benchmarks/run_bclconvert.L003.0007_tiles0589-0686.bench.tsv
    reason: Missing output files: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_fastqs/L003/0007_tiles0589-0686/Reports/fastq_list.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_fastqs/L003/0007_tiles0589-0686/Reports/Demultiplex_Stats.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_reports/L003/0007_tiles0589-0686/bclconvert.done; 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=0007_tiles0589-0686
    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/L003/0007_tiles0589-0686 results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/normalized.SampleSheet.csv 3 results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_reports/L003/0007_tiles0589-0686/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.L003.0007_tiles0589-0686.log results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_fastqs/L003/0007_tiles0589-0686/Reports/fastq_list.csv results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_fastqs/L003/0007_tiles0589-0686/Reports/Demultiplex_Stats.csv results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_reports/L003/0007_tiles0589-0686/bclconvert.done 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_2349+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_2358+s_3_2359+s_3_2360+s_3_2361+s_3_2362+s_3_2363+s_3_2364+s_3_2365+s_3_2366+s_3_2367+s_3_2368+s_3_2369+s_3_2370+s_3_2371+s_3_2372+s_3_2373+s_3_2374+s_3_2375+s_3_2376+s_3_2377+s_3_2378+s_3_2379+s_3_2380+s_3_2381+s_3_2382+s_3_2383+s_3_2384+s_3_2385+s_3_2386+s_3_2387+s_3_2388+s_3_2389+s_3_2390+s_3_2391+s_3_2392+s_3_2393+s_3_2394+s_3_2395+s_3_2396+s_3_2397+s_3_2398
Submitted job 10 with external jobid '83'.

[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/L003/0004_tiles0295-0392/bclconvert.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tile_fastqs/L003/0004_tiles0295-0392/Reports/fastq_list.csv, results/runs/2--output truncated--
