gem-pasteur/Integron_Finder

Issues

• [BUG] IF crashes with --gbk option in a specific caase

  #104 opened 6 months ago by eloilit
  3

• [BUG] Error in find_attc_max function

  #117 opened 6 months ago by Ales-ibt
  5

• [BUG] Wrong coordinates in results

  #114 opened 6 months ago by fmalmeida
  13

• How to classify Integrons？

  #116 opened 8 months ago by xdli009
  1

• ValueError: attempt to get argmin of an empty sequence

  #92 opened 3 years ago by danyu-uofa
  4

• [FEAT] specify output folder or path

  #115 opened 9 months ago by susheelbhanu
  1

• [FEAT] improve IF to work with gembase 2

  #112 opened 10 months ago by bneron
  0

• [FEAT] Use the option --prot-file independently of the option --annot-parser

  #113 opened a year ago by LCoffion
  0

• Integron_Finder bogs down server's I/O when ran on metagenomes with ~million contigs

  #90 opened 3 years ago by JuntaoZhong
  3

• [FEAT] Remove/Relax Matplotlib version requirement

  #111 opened a year ago by acarafat
  5

• [BUG] IF crashes on a multiple contigs file

  #103 opened a year ago by eloilit
  1

• [HELP] Different results in hits between multi-gbk and merged gbk on same sample?

  #109 opened a year ago by Svnipni
  2

• [HELP] In silico IntI1 qPCR assay don't match results IntegronFinder

  #110 opened a year ago by LauraVP1994
  10

• AttributeError: module 'Bio.Seq' has no attribute 'IUPAC'

  #108 opened a year ago by EllBaum
  2

• [HELP] How can I get the sequence of whole integron?

  #105 opened 2 years ago by Galib009
  3

• [BUG] underlay of /etc/localtime required more than 50 (87) bind mounts

  #107 opened 2 years ago by yegonzalezflores
  4

• How to use --func-annot

  #106 opened 2 years ago by aslangabriel
  1

• [HELP] Question: are the integrase (IntI) always on the opposite strand of gene cassettes?

  #101 opened 2 years ago by jiarong
  3

• [HELP] Question: are gene cassettes of a integron all on the same strand?

  #102 opened 2 years ago by jiarong
  4

• [FEAT] genbank or gff as input

  #100 opened 2 years ago by alexweisberg
  0

• [BUG] IntegronFinder fails when there is a "space" in the path

  #99 opened 2 years ago by eloilit
  1

• [FEAT] Add documentation about CPU usage

  #97 opened 2 years ago by eloilit
  0

• install Integron_Finder through conda

  #96 opened 3 years ago by danielarothschild
  0

• Complete documentation for ARG

  #95 opened 3 years ago by jeanrjc
  1

• IntegronFinder does not pass unitary test "test_main_outdir_exists" (test_merge.TestMain)

  #94 opened 3 years ago by eloilit
  0

• problem with overlapping/near identical attC sites

  #69 opened 3 years ago by jeanrjc
  6

• IntegronFinder should not run twice over the the edge of the replicon

  #88 opened 3 years ago by jeanrjc
  0

• Error running Singularity

  #76 opened 3 years ago by ramadatta
  4

• Issue with colorlog logging

  #93 opened 3 years ago by alexweisberg
  1

• Problem installing integron_finder via bioconda

  #82 opened 4 years ago by evolarjun
  5

• IF give different results depending installation

  #91 opened 3 years ago by bneron
  2

• update hmmsearch command line and profile

  #89 opened 3 years ago by bneron
  0

• Keep attC sites even if the evalue change with local_max

  #84 opened 3 years ago by jeanrjc
  0

• Topology issues

  #70 opened 3 years ago by jeanrjc
  2

• in summary output, add the size of contig

  #68 opened 3 years ago by jeanrjc
  0

• error on calling --gembases option

  #80 opened 3 years ago by cachapuz2001
  1

• go_left = (full_element[full_element.type_elt == "attC"].pos_beg.values[0] - df_max.pos_end.values[0]: index 0 is out of bounds for axis 0 with size 0

  #73 opened 3 years ago by vbrover
  6

• Fatal error: Exit code 127 ()

  #86 opened 4 years ago by IustinBilavschi
  1

• Help me understanding the output of IF with a multi-fasta file

  #87 opened 4 years ago by bramvandijk88
  2

• End location (191284) must be greater than or equal to start location (271412)

  #85 opened 4 years ago by erichy91
  6

• IndexError attc.py

  #71 opened 4 years ago by jfourquet2
  4

• Error related to prodigal: RuntimeError("{0} failed returncode = {1}".format(prodigal_cmd, returncode))

  #79 opened 4 years ago by sasonbol
  16

• some major and common problems

  #81 opened 4 years ago by hongyuan-zheng
  2

• program not work for Staphylococcus aureus

  #83 opened 4 years ago by wmbio
  1

• AttributeError: module 'Bio.Seq' has no attribute 'IUPAC'

  #78 opened 4 years ago by deoliveiralab
  4

• conda install causes pandas.io.common ImportError

  #77 opened 4 years ago by nebfield
  2

• ID_integron should not be in .summary file

  #67 opened 5 years ago by jeanrjc
  1

• Integron classes 1,2,3

  #75 opened 5 years ago by koopkaup
  1

• Installing from pip not working

  #74 opened 5 years ago by leaemiliepradier
  3

• "integron_finder --local_max --func_annot mysequences.fst" should be "integron_finder --local-max --func-annot mysequences.fst"

  #72 opened 5 years ago by vbrover
  0