## ONT retry1
            echo "ERROR: Failed to create TMPDIR: $TMPDIR" >> results/day/hg38_broad/ONT-4Coriells-chip2-NA03986-DMPK-chip2-barcode20-chip2-0000-PF-ONT-PROMETHION/align/sentmm2ont/logs/ONT-4Coriells-chip2-NA03986-DMPK-chip2-barcode20-chip2-0000-PF-ONT-PROMETHION.sentmm2ont_sort.log 2>&1;
            echo "ERROR: TMPDIR disappeared before pipeline start: $tdir" >> results/day/hg38_broad/ONT-4Coriells-chip2-NA03986-DMPK-chip2-barcode20-chip2-0000-PF-ONT-PROMETHION/align/sentmm2ont/logs/ONT-4Coriells-chip2-NA03986-DMPK-chip2-barcode20-chip2-0000-PF-ONT-PROMETHION.sentmm2ont_sort.log 2>&1;
                echo "ERROR: unsupported sentmm2ont input kind: fastq" >> results/day/hg38_broad/ONT-4Coriells-chip2-NA03986-DMPK-chip2-barcode20-chip2-0000-PF-ONT-PROMETHION/align/sentmm2ont/logs/ONT-4Coriells-chip2-NA03986-DMPK-chip2-barcode20-chip2-0000-PF-ONT-PROMETHION.sentmm2ont_sort.log 2>&1;
Submitted job 1466 with external jobid '51'.
Finished job 582.
rule sentmm2ont_align_sort:
        ulimit -n 65536 || echo "ulimit mod failed";
            echo "ERROR: Failed to create TMPDIR: $TMPDIR" >> results/day/hg38_broad/ONT-4Coriells-chip1-NA03986-DMPK-chip1-barcode20-chip1-0023-PF-ONT-PROMETHION/align/sentmm2ont/logs/ONT-4Coriells-chip1-NA03986-DMPK-chip1-barcode20-chip1-0023-PF-ONT-PROMETHION.sentmm2ont_sort.log 2>&1;
            echo "ERROR: TMPDIR disappeared before pipeline start: $tdir" >> results/day/hg38_broad/ONT-4Coriells-chip1-NA03986-DMPK-chip1-barcode20-chip1-0023-PF-ONT-PROMETHION/align/sentmm2ont/logs/ONT-4Coriells-chip1-NA03986-DMPK-chip1-barcode20-chip1-0023-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-chip1-0023-PF-ONT-PROMETHION/align/sentmm2ont/logs/ONT-4Coriells-chip1-NA03986-DMPK-chip1-barcode20-chip1-0023-PF-ONT-PROMETHION.sentmm2ont_sort.log 2>&1;
Submitted job 390 with external jobid '52'.
Finished job 586.
rule sentmm2ont_align_sort:
        ulimit -n 65536 || echo "ulimit mod failed";
            echo "ERROR: Failed to create TMPDIR: $TMPDIR" >> results/day/hg38_broad/ONT-4Coriells-chip1-NA03986-DMPK-chip1-barcode20-chip1-0012-PF-ONT-PROMETHION/align/sentmm2ont/logs/ONT-4Coriells-chip1-NA03986-DMPK-chip1-barcode20-chip1-0012-PF-ONT-PROMETHION.sentmm2ont_sort.log 2>&1;
## ILMN
Submitted job 5 with external jobid '15'.
rule sentieon_bwa_sort:
        ulimit -n 65536 || echo "ulimit mod failed" > results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-HG003-c-GIAB-all-S9-PF-ILMN-NOVASEQ/align/sent/logs/20260526-LH01121-0004-B23WW2NLT4-HG003-c-GIAB-all-S9-PF-ILMN-NOVASEQ.sent.sort.log 2>&1;
Submitted job 20 with external jobid '16'.
rule sentieon_bwa_sort:
        ulimit -n 65536 || echo "ulimit mod failed" > results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA05164-DMPK-all-S49-PF-ILMN-NOVASEQ/align/sent/logs/20260526-LH01121-0004-B23WW2NLT4-NA05164-DMPK-all-S49-PF-ILMN-NOVASEQ.sent.sort.log 2>&1;
