TobyBaril/EarlGrey

Issues

• Singularity container initial setup not working

  #138 opened 2 months ago by MikeSanJose
  11

• Resume from in-progress TEStrainer iterations

  #145 opened 2 months ago by mjacksonhill
  2

• RepeatModeler or RepeatMasker failed with EarlGrey v4.4.0 and RepeatMasker v4.15, lanscape.pdf missed and an extended runtime of RepeatModeler round with EarlGrey v4.4.0 and RepeatMasker v4.15

  #140 opened 2 months ago by manwensu
  4

• runtime in TEstrainer ultralong for *some* genomes

  #135 opened 3 months ago by estolle
  6

• Long running time

  #139 opened 2 months ago by sherlock0088
  3

• sa-ssr: command not found

  #137 opened 2 months ago by r-mashoodh
  2

• The progress appears quite slow for large genome

  #144 opened 2 months ago by joweihsieh
  1

• Out of Memory but the job seemed already finished

  #143 opened 2 months ago by ting-hsuan-chen
  7

• Conda install error

  #128 opened 3 months ago by Glfrey
  6

• RepeatMasker complains about invalid species search term (but runs at Gitpod)

  #136 opened 3 months ago by trypchromics
  5

• Warning: malformed fasta index file

  #134 opened 2 months ago by JonEilers
  3

• RepeatModeler always runs with 1 thread, does not reuse earlier round results

  #131 opened 3 months ago by mjacksonhill
  4

• Only generating pie plot and no other summary plots

  #126 opened 3 months ago by johannabeam
  4

• unclassified TE

  #133 opened 3 months ago by PengfeiInTuebingen
  1

• can not generate Repeat Landscapes showing TE activity

  #132 opened 3 months ago by skuri1222
  2

• Summary plot fails because `bc` is missing (maybe)

  #118 opened 3 months ago by chriswyatt1
  5

• perl locale warning in Singularity container

  #130 opened 3 months ago by mjacksonhill
  2

• Calculation of LTR insertion time

  #122 opened 4 months ago by JMUwenjian
  2

• Update soft masking option to avoid maskfasta bug

  #129 opened 4 months ago by DustinSokolowski
  0

• Gff3 Question

  #127 opened 4 months ago by sherlock0088
  1

• ModuleNotFoundError at TEstrainer stage

  #120 opened 4 months ago by kiran-lee
  8

• [E::fai_read] Could not understand FASTA index and RepeatLandscape

  #121 opened 4 months ago by enriquepola1996
  7

• -recoverDir option for RepeatModeler?

  #125 opened 4 months ago by r-mashoodh
  2

• EG4.0.8 vs EG 4.2.4

  #116 opened 5 months ago by ekaralashvili
  3

• RepeatMasker fails upon finishing

  #112 opened 5 months ago by DrPintoThe2nd
  5

• Compared with repeatmodeler + repeatmasker, earlgrey annotated the bases masked of the transposon at a lower proportion

  #117 opened 5 months ago by wanjiujiu
  5

• overextension of TEs

  #115 opened 5 months ago by ferrojm
  2

• data for pie chart proportions

  #105 opened 5 months ago by baligpanossian
  9

• Relaunching divergence calculation

  #113 opened 5 months ago by SwiftSeal
  5

• annotations in gff file not shown in IGV

  #111 opened 5 months ago by ting-hsuan-chen
  3

• Question about error

  #110 opened 6 months ago by mylena-s
  2

• Installation Errors following "Earl Grey Installation and Configuration (If you already have RepeatMasker and RepeatModeler)"

  #109 opened 6 months ago by ufaroooq
  2

• impact of initial ,masking by RM and usage of DFAM3.8

  #107 opened 6 months ago by estolle
  5

• RepeatModeler run successfully, but did not create *.classified file and *-families.fa, and so stopped the earlGrey.

  #108 opened 6 months ago by jaehakson
  8

• Stuck at the "Cleaning Genome" phase

  #104 opened 7 months ago by rpianezza
  7

• Variation in annotation within species/family

  #97 opened 7 months ago by lesserof2weevils
  2

• Bug when using soft link to genome

  #102 opened 7 months ago by mylena-s
  1

• Filtering overlapping repeats for chimers

  #95 opened 7 months ago by pellescholten
  3

• Generate soft-masked genome without re-running?

  #100 opened 7 months ago by YingChen94
  2

• GFF attributes and wrong TE classification??

  #99 opened 7 months ago by DhakadPankaj
  1

• R step 12 "no"?

  #98 opened 7 months ago by YingChen94
  1

• Limiting Repeatmodeler rounds to 4/5 ??

  #96 opened 7 months ago by DhakadPankaj
  3

• Error while using a custom library

  #94 opened 8 months ago by azotta
  2

• underprediction

  #91 opened 8 months ago by estolle
  3

• Kimura expectations

  #92 opened 8 months ago by TCHeaven
  0

• Runtime and Restarting

  #93 opened 8 months ago by rpyron
  1

• why so many 'unknown' sequences in generated TE lib

  #90 opened 8 months ago by Yiguan
  2

• TRFMask issue, files not found

  #87 opened 9 months ago by Sandandsnow2004
  5

• Annotation accuracy

  #89 opened 9 months ago by Song-10-YF
  1

• Errors in the log file

  #88 opened 9 months ago by ekaralashvili
  1