Lcornet/GENERA

Issues

• Metabolic modelling - job still running even if error when processing one of the bins

  #46 opened a month ago by chbalent
  2

• Busco - extra line for "list" in results - seems to work best with one bin at a time

  #45 opened 2 months ago by chbalent
  0

• A new binner for long reads

  #44 opened 2 months ago by chbalent
  0

• Sambamba instead of samtools sort for Mapping of longreads in assembly

  #43 opened 2 months ago by chbalent
  0

• Illumina Assembly of metagenome with MEGAHIT - Segmentation fault

  #42 opened 4 months ago by chbalent
  0

• Orthology output

  #41 opened 4 months ago by chbalent
  0

• Metabolic tool : option to make a gff output (for mantis)

  #40 opened a year ago by SRibeiroMonteiro
  0

• Braker

  #39 opened a year ago by FreBaert
  1

• Phylogeny empty alignment

  #33 opened 2 years ago by FreBaert
  10

• Quality assesment genomes parameter bug

  #38 opened 2 years ago by FreBaert
  1

• orthoANI heatmap issue

  #37 opened 2 years ago by FreBaert
  1

• Phylogeny: Error executing process > concatenation (1) (Empty sequence for GCF_genome@id)

  #35 opened 2 years ago by SinaedaA
  8

• DNA mode phylogeny

  #36 opened 2 years ago by FreBaert
  1

• heatmap.pdf with no "row.names"

  #34 opened 2 years ago by SinaedaA
  1

• Error in `levels<-`(`*tmp*`, value = as.character(levels)) : factor level [12] is duplicated

  #32 opened 2 years ago by SinaedaA
  9

• disk quota?

  #31 opened 2 years ago by FreBaert
  1

• Assembly seems stuck at Trimming step

  #30 opened 2 years ago by FreBaert
  8

• unzipping files

  #29 opened 2 years ago by edhooge
  9

• 10. Annotation question

  #27 opened 2 years ago by icleenwe
  5

• New assembler for GENERA Assembly

  #1 opened 3 years ago by Lcornet
  1

• BUSCO permission

  #23 opened 3 years ago by Lcornet
  1

• BUSCO failed : AttributeError: module '__main__' has no attribute '__spec__'

  #26 opened 3 years ago by bdurieu
  3

• eukcc

  #25 opened 3 years ago by FreBaert
  1

• GENcontams job contains typo

  #24 opened 3 years ago by FreBaert
  1

• organism parameter

  #9 opened 3 years ago by FreBaert
  10

• annotation - fastq-dump error

  #19 opened 3 years ago by edhooge
  2

• fastqdump: 'timeout exhausted' - issue

  #14 opened 3 years ago by edhooge
  3

• Add version of scripts

  #4 opened 3 years ago by Lcornet
  1

• Closest match in ANI delete duplicate assemblies

  #22 opened 3 years ago by Lcornet
  1

• file extention for orthology

  #12 opened 3 years ago by FreBaert
  2

• Genome assembly fastp command not found

  #21 opened 3 years ago by FreBaert
  3

• Genome downloader issue

  #20 opened 3 years ago by FreBaert
  2

• genome assembly - shortreadassembly doesn't work

  #18 opened 3 years ago by edhooge
  2

• species filter in Genome_dw

  #5 opened 3 years ago by Lcornet
  1

• Add DREP

  #17 opened 3 years ago by Lcornet
  1

• Orthology core genes question

  #15 opened 3 years ago by FreBaert
  5

• Multi-locus Phylogeny ML

  #8 opened 3 years ago by Lcornet
  1

• Phylogeny DNA mode

  #16 opened 3 years ago by FreBaert
  2

• rep parameter for jackknife

  #13 opened 3 years ago by FreBaert
  3

• path for the assembly suite is not recognized

  #11 opened 3 years ago by edhooge
  1

• Annotation empty output

  #10 opened 3 years ago by FreBaert
  2

• Annotation file not found

  #7 opened 3 years ago by FreBaert
  1

• Error in wiki for Annotation

  #6 opened 3 years ago by FreBaert
  1

• Genome downloader isn't working

  #3 opened 3 years ago by edhooge
  20

• How to cite

  #2 opened 3 years ago by Lcornet
  1