Submitted job 596 with external jobid '13'.
rule fastqc_subsampled:
Submitted job 583 with external jobid '14'.
Finished job 21.
Finished job 9.
Finished job 15.
Finished job 39.
Finished job 45.
Finished job 33.
Finished job 658.
Finished job 27.
Finished job 8.
localrule workflow_staging:
Finished job 7.
Job 6: You can override the defalt mesage output to the terminal per rule execution if you wish, including wildcards and config variables.  This is for sample sample.
        ( mkdir -p $(dirname results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-HG003-a-GIAB-all-S7-PF-ILMN-NOVASEQ/20260526-LH01121-0004-B23WW2NLT4-HG003-a-GIAB-all-S7-PF-ILMN-NOVASEQ.dirsetup.ready results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ/20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ.dirsetup.ready results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-HG003-c-GIAB-all-S9-PF-ILMN-NOVASEQ/20260526-LH01121-0004-B23WW2NLT4-HG003-c-GIAB-all-S9-PF-ILMN-NOVASEQ.dirsetup.ready results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA00232-SMN-all-S46-PF-ILMN-NOVASEQ/20260526-LH01121-0004-B23WW2NLT4-NA00232-SMN-all-S46-PF-ILMN-NOVASEQ.dirsetup.ready results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ/20260526-LH01121-0004-B23WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ.dirsetup.ready results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA05164-DMPK-all-S49-PF-ILMN-NOVASEQ/20260526-LH01121-0004-B23WW2NLT4-NA05164-DMPK-all-S49-PF-ILMN-NOVASEQ.dirsetup.ready results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA09677-SMN-all-S47-PF-ILMN-NOVASEQ/20260526-LH01121-0004-B23WW2NLT4-NA09677-SMN-all-S47-PF-ILMN-NOVASEQ.dirsetup.ready ) || echo "ERROR:: mkdir $(dirname results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-HG003-a-GIAB-all-S7-PF-ILMN-NOVASEQ/20260526-LH01121-0004-B23WW2NLT4-HG003-a-GIAB-all-S7-PF-ILMN-NOVASEQ.dirsetup.ready results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ/20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ.dirsetup.ready results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-HG003-c-GIAB-all-S9-PF-ILMN-NOVASEQ/20260526-LH01121-0004-B23WW2NLT4-HG003-c-GIAB-all-S9-PF-ILMN-NOVASEQ.dirsetup.ready results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA00232-SMN-all-S46-PF-ILMN-NOVASEQ/20260526-LH01121-0004-B23WW2NLT4-NA00232-SMN-all-S46-PF-ILMN-NOVASEQ.dirsetup.ready results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ/20260526-LH01121-0004-B23WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ.dirsetup.ready results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA05164-DMPK-all-S49-PF-ILMN-NOVASEQ/20260526-LH01121-0004-B23WW2NLT4-NA05164-DMPK-all-S49-PF-ILMN-NOVASEQ.dirsetup.ready results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA09677-SMN-all-S47-PF-ILMN-NOVASEQ/20260526-LH01121-0004-B23WW2NLT4-NA09677-SMN-all-S47-PF-ILMN-NOVASEQ.dirsetup.ready )  FAILED";
Finished job 6.
rule sentieon_bwa_sort:
        ulimit -n 65536 || echo "ulimit mod failed" > results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-HG003-a-GIAB-all-S7-PF-ILMN-NOVASEQ/align/sent/logs/20260526-LH01121-0004-B23WW2NLT4-HG003-a-GIAB-all-S7-PF-ILMN-NOVASEQ.sent.sort.log 2>&1;
