## ONT retry1
            echo "ERROR: TMPDIR disappeared before pipeline start: $tdir" >> results/day/hg38_broad/ONT-4Coriells-chip1-NA03986-DMPK-chip1-barcode20-chip1-0009-PF-ONT-PROMETHION/align/sentmm2ont/logs/ONT-4Coriells-chip1-NA03986-DMPK-chip1-barcode20-chip1-0009-PF-ONT-PROMETHION.sentmm2ont_sort.log 2>&1;
                echo "ERROR: unsupported sentmm2ont input kind: fastq" >> results/day/hg38_broad/ONT-4Coriells-chip1-NA03986-DMPK-chip1-barcode20-chip1-0009-PF-ONT-PROMETHION/align/sentmm2ont/logs/ONT-4Coriells-chip1-NA03986-DMPK-chip1-barcode20-chip1-0009-PF-ONT-PROMETHION.sentmm2ont_sort.log 2>&1;
Submitted job 334 with external jobid '79'.
Finished job 2698.
rule sentmm2ont_align_sort:
        ulimit -n 65536 || echo "ulimit mod failed";
            echo "ERROR: Failed to create TMPDIR: $TMPDIR" >> results/day/hg38_broad/ONT-4Coriells-chip4-NA03986-DMPK-chip4-barcode20-chip4-0010-PF-ONT-PROMETHION/align/sentmm2ont/logs/ONT-4Coriells-chip4-NA03986-DMPK-chip4-barcode20-chip4-0010-PF-ONT-PROMETHION.sentmm2ont_sort.log 2>&1;
            echo "ERROR: TMPDIR disappeared before pipeline start: $tdir" >> results/day/hg38_broad/ONT-4Coriells-chip4-NA03986-DMPK-chip4-barcode20-chip4-0010-PF-ONT-PROMETHION/align/sentmm2ont/logs/ONT-4Coriells-chip4-NA03986-DMPK-chip4-barcode20-chip4-0010-PF-ONT-PROMETHION.sentmm2ont_sort.log 2>&1;
                echo "ERROR: unsupported sentmm2ont input kind: fastq" >> results/day/hg38_broad/ONT-4Coriells-chip4-NA03986-DMPK-chip4-barcode20-chip4-0010-PF-ONT-PROMETHION/align/sentmm2ont/logs/ONT-4Coriells-chip4-NA03986-DMPK-chip4-barcode20-chip4-0010-PF-ONT-PROMETHION.sentmm2ont_sort.log 2>&1;
Submitted job 2710 with external jobid '80'.
Finished job 1502.
rule sentmm2ont_align_sort:
        ulimit -n 65536 || echo "ulimit mod failed";
            echo "ERROR: Failed to create TMPDIR: $TMPDIR" >> results/day/hg38_broad/ONT-4Coriells-chip4-NA03986-DMPK-chip4-barcode20-chip4-0009-PF-ONT-PROMETHION/align/sentmm2ont/logs/ONT-4Coriells-chip4-NA03986-DMPK-chip4-barcode20-chip4-0009-PF-ONT-PROMETHION.sentmm2ont_sort.log 2>&1;
## ILMN
Submitted job 32 with external jobid '21'.
Building DAG of jobs...
Finished job 597.
Finished job 595.
Finished job 594.
Finished job 596.
Finished job 591.
Finished job 593.
Finished job 590.
Finished job 592.
localrule compile_seqfu:
Finished job 589.
Finished job 38.
rule no_dedup:
Submitted job 630 with external jobid '62'.
rule doppelmark_dups:
        ulimit -n 65536 || echo "ulimit mod failed" > results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA05164-DMPK-all-S49-PF-ILMN-NOVASEQ/align/sent/dmd/logs/dedupe.dmd.20260526-LH01121-0004-B23WW2NLT4-NA05164-DMPK-all-S49-PF-ILMN-NOVASEQ.sent.log 2>&1;
