1c0824920cd06057c2e7c02d9cb7ecc153a99d5e hiram Fri Sep 25 14:00:59 2026 -0700 please no ssh from cluster nodes back to hgwdev to run hgsql commands refs #34360 diff --git src/hg/utils/automation/doMiniMap2.pl src/hg/utils/automation/doMiniMap2.pl index 779ad99ca2f..b552c8624bf 100755 --- src/hg/utils/automation/doMiniMap2.pl +++ src/hg/utils/automation/doMiniMap2.pl @@ -689,35 +689,31 @@ close($fh); if ($line =~ /^mashDistance=(\S+)\s+minimapPreset=(\S+)/) { $minimapPreset = $2; &HgAutomate::verbose(1, "Reusing cached mash distance $1 -> " . "-minimapPreset=$minimapPreset from $mashFile\n"); return; } } if ($opt_debug) { $minimapPreset = 'asm5'; &HgAutomate::verbose(1, "-debug: skipping mash, using -minimapPreset=$minimapPreset\n"); return; } &HgAutomate::verbose(1, "Estimating $tDb/$qDb divergence with mash to pick -minimapPreset ...\n"); - # $dbHost matters here: hgcentraltest (used to recognize a plain UCSC - # db's own .2bit) is only reachable from hgwdev, never from whatever - # host might eventually run this -- pass our own $dbHost through - # rather than let AssemblyDivergence.pm assume one. - my $dist = eval { &AssemblyDivergence::mashDistance($tSeq, $qSeq, $buildDir, $opt_regenerateMash, $dbHost); }; + my $dist = eval { &AssemblyDivergence::mashDistance($tSeq, $qSeq, $buildDir, $opt_regenerateMash); }; if ($@) { $minimapPreset = 'asm5'; warn "estimateDivergence: $@" . "falling back to -minimapPreset=$minimapPreset. Pass " . "-minimapPreset explicitly to pick it yourself and silence this.\n"; return; } my ($pipeline, $preset, $warning) = &AssemblyDivergence::choosePipeline($dist); warn "$warning\n" if ($warning); if ($pipeline ne 'minimap2') { die "estimateDivergence: mash distance $dist between $tDb and $qDb " . "looks too diverged for doMiniMap2.pl -- use doBlastzChainNet.pl " . "instead, or re-run with -minimapPreset to force minimap2 anyway.\n"; } $minimapPreset = $preset;