Issues

• ALIGNMENT PIPELINE ERROR

  churchlab/millstone#711 · Filter by author seamyname opened on Mar 4, 2022
  2

• Problem uploading samples

  churchlab/millstone#701 · Filter by author Zymergen-SBRUBAKER opened on Oct 31, 2019
  36

• Files uploaded through browser remain in /tmp after completion

  bug
  churchlab/millstone#700 · Filter by author glebkuznetsov opened on Apr 6, 2018

• Generate New Reference Genome: ERROR: More than one record found in handle

  churchlab/millstone#699 · Filter by author bfurtwa opened on Mar 7, 2018
  5

• How is extremely high-coverage defined?

  churchlab/millstone#698 · Filter by author bfurtwa opened on Mar 7, 2018
  1

• jbrowse contig fail

  churchlab/millstone#696 · Filter by author MaxSchubert opened on Nov 13, 2017

• filter key Gene non-functional

  churchlab/millstone#695 · Filter by author MaxSchubert opened on Nov 10, 2017

• Genbank exported from latest version of Geneious appears to cause error

  churchlab/millstone#694 · Filter by author glebkuznetsov opened on Jul 13, 2017

• OptMAGE only works with MG1655

  churchlab/millstone#691 · Filter by author dbgoodman opened on Jan 23, 2017

• OptMAGE support doesn't work for multi-bp SNVs

  churchlab/millstone#690 · Filter by author dbgoodman opened on Jan 23, 2017

• Jbrowse tracks for deleted alignments get left behind

  churchlab/millstone#689 · Filter by author dbgoodman opened on Oct 12, 2016

• Make queries be case insensitive

  low priority
  churchlab/millstone#688 · Filter by author dbgoodman opened on Sep 27, 2016

• Velvetg runs out of memory during graph building

  bug
  churchlab/millstone#687 · Filter by author glebkuznetsov opened on Sep 15, 2016

• Contig calling shows QUEUED_TO_ASSEMBLE even though really ASSEMBLING, sometimes.

  bug
  churchlab/millstone#686 · Filter by author glebkuznetsov opened on Jun 24, 2016

• JBrowse warning when re-running contig pipeline

  bug
  churchlab/millstone#685 · Filter by author glebkuznetsov opened on Jun 23, 2016
  2

• On variant csv export, what to do about LONG REF/ALT alleles?

  bug
  churchlab/millstone#683 · Filter by author dbgoodman opened on Jun 21, 2016

• If materialization is kicked off from the variant view UI, and page is refreshes, materialization happens again and they collide.

  bug
  churchlab/millstone#677 · Filter by author dbgoodman opened on Jun 9, 2016
  3

• Look into custom SV calling pipeline parallelization.

  bug
  churchlab/millstone#676 · Filter by author glebkuznetsov opened on Jun 9, 2016

• Mobile Element finding crashes when contigs are identified across two IS elements

  bug
  churchlab/millstone#675 · Filter by author dbgoodman opened on Jun 1, 2016

• Make SVs from Brian's Pipeline flip the IS_SV flag

  bugsv_cleanup
  churchlab/millstone#673 · Filter by author dbgoodman opened on May 30, 2016

• Annotation on SVs (maybe SnpEff?)

  enhancementsv_cleanup
  churchlab/millstone#672 · Filter by author glebkuznetsov opened on May 30, 2016

• Need to be more stringent when calling deletions using low coverage

  bugsv_cleanup
  churchlab/millstone#671 · Filter by author glebkuznetsov opened on May 30, 2016
  1

• Millstone does not like certain .gb template files, throws "next iteration" error

  bug
  churchlab/millstone#669 · Filter by author mnapolitano89 opened on May 26, 2016
  2

• Millstone not collecting unused reads for contig assembly use

  bug
  churchlab/millstone#668 · Filter by author mnapolitano89 opened on May 26, 2016
  4

• Make SnpEff an option the user can control

  enhancement
  churchlab/millstone#667 · Filter by author glebkuznetsov opened on May 23, 2016