ncbi/pgap

Issues

• [BUG] Annotation fails, cause mysterious

  #323 opened a month ago by dlhuseby29
  28

• [BUG] Installation fails

  #324 opened a month ago by mau-olvera
  3

• Error: Final process status is permanentFail

  #304 opened 6 months ago by sekhwal
  16

• [BUG] <title>

  #322 opened a month ago by Artifice120
  3

• PGAP failed on metatranscriptome data

  #318 opened a month ago by asifratul
  1

• [BUG] --update failed

  #321 opened a month ago by XMUykyz
  1

• [BUG] A YAML file argument cannot be used in combination with either the -s/--organism or -g/--genome arguments

  #294 opened 7 months ago by TCHeaven
  26

• [BUG] A YAML file argument cannot be used in combination with either the -s/--organism or -g/--genome arguments. The -s/--organism and the -g/--genome arguments replace the YAML file argument input.

  #320 opened 2 months ago by yulinpengcool
  4

• [BUG] <title>PGAP failed

  #316 opened 2 months ago by StickHu
  5

• [BUG] <title> installation failed

  #319 opened 2 months ago by BlackMonolith
  3

• [BUG] Docker exited with rc = 1

  #317 opened 2 months ago by skyds4499
  4

• [BUG] PGAP failed, docker exited with rc = 1

  #315 opened 3 months ago by AnmotCar
  11

• [BUG] GFF3 output file does not contain sequence-region name

  #314 opened 3 months ago by watsonar
  3

• [BUG] FATAL: "cwltool": executable file not found in $PATH in 2024-04-27.build7426

  #313 opened 3 months ago by komais
  4

• [BUG] PGAP fails on test genome when PGAP_INPUT_DIR set to other than default

  #310 opened 4 months ago by mdziurzynski
  4

• [BUG] When two input genomes have same basename, the first genome is mistakenly used for the second run.

  #273 opened 4 months ago by pvstodghill
  4

• [BUG] Fail in GenBank output file

  #296 opened 4 months ago by juansebe1
  9

• [BUG] Failing to run some sequences

  #312 opened 4 months ago by jmemrava
  2

• ORF prediction issue

  #308 opened 4 months ago by tangwei825
  3

• Get_Proteins_app issues

  #303 opened 4 months ago by asd1864714
  14

• [BUG] Genus species requirement

  #309 opened 4 months ago by rsieskind
  8

• Species_Requirement_option

  #311 opened 4 months ago by cristoyerenahs
  1

• PGAP for multiple users

  #307 opened 6 months ago by vappiah
  2

• Error: Final process status is permanentFail

  #305 opened 6 months ago by sekhwal
  17

• source code for gc_get_molecules

  #306 opened 6 months ago by OH-AU
  2

• [Error] Docker exited with rc = 1

  #301 opened 6 months ago by namho4577
  3

• [Error] Docker exited with rc =1

  #302 opened 6 months ago by namho4577
  2

• [BUG] Final process status is permanentFail

  #300 opened 6 months ago by namho4577
  1

• product protein name issues

  #298 opened 6 months ago by asd1864714
  3

• [BUG] -c flag not received: /mnt/shared/scratch/theaven/uncompressed/hogenhout/pgap-s7

  #295 opened 7 months ago by TCHeaven
  1

• [BUG] checkm dies with "OSError: AF_UNIX path too long"

  #288 opened 7 months ago by MrTomRod
  5

• pgap --update showing huge file size during installation

  #292 opened 7 months ago by Sabarish2001
  19

• [BUG] Failing to run my own sequence

  #290 opened 8 months ago by kfsb
  19

• Running PGAP with Metagenomic Assembled Genome

  #275 opened 8 months ago by kevinmyers
  11

• [FEATURE REQUEST] Support for Charlie Cloud Docker compatible (but more secure) container system for HPC

  #291 opened 8 months ago by idlfuente
  1

• [BUG] <title>The length of the gene exceeds the length of the conitg

  #282 opened 8 months ago by Moo-cow
  10

• [BUG] <title>How to run pgap.py with qsub file.

  #284 opened 8 months ago by wurunbiao162
  5

• [FEATURE REQUEST] Quit if no SSE4.2 support is detected

  #287 opened 9 months ago by MrTomRod
  6

• [FEATURE REQUEST] Workaround for "taskset: failed to set pid 0's affinity"-Bug

  #289 opened 9 months ago by MrTomRod
  2

• [BUG] WARNING Final process status is permanentFail

  #286 opened 9 months ago by snackens
  9

• [FEATURE REQUEST] <Turn Off GO annotation>

  #280 opened 9 months ago by greg-harhay
  7

• [BUG] pgap.py --update

  #271 opened 9 months ago by nptgiang0211
  3

• [BUG] PGAP analysis generates all files except .aa and .gbk

  #276 opened 9 months ago by Chahrazadt87
  35

• Problem with running pgap annotation

  #278 opened 9 months ago by Subhajeet1997
  1

• [FEATURE REQUEST] direct S3 access to input datasets

  #274 opened 10 months ago by jvolkening
  5

• PIPELINE TEST w/ M. genitalium - PermissionError: [Errno 13] Permission denied: '/pgap/output/debug/tmpdir

  #283 opened 10 months ago by raysully
  38

• [FEATURE REQUEST] Unable to retrieve additional reference data from https://s3.amazonaws.com/pgap/input-[version].tgz.

  #277 opened a year ago by Tayvich
  2

• [BUG] Binding non-existent file

  #281 opened a year ago by kkrick-sdsu
  6

• [FEATURE REQUEST] Any plans about EGAP (Eukaryotic Genome Annotation Pipeline)?

  #279 opened a year ago by GRGong
  2

• [BUG] PGAP fails install when running on singularity.

  #272 opened a year ago by Ge0rges
  2