ncbi pgap issues - Githubissues

ncbi / pgap

NCBI Prokaryotic Genome Annotation Pipeline

Other

301 stars 89 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

[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 yulinpengcool opened 11 hours ago
0
[BUG] <title> installation failed

#319 BlackMonolith opened 15 hours ago
0
PGAP failed on metatranscriptome data

#318 asifratul opened 4 days ago
0
[BUG] Docker exited with rc = 1

#317 skyds4499 closed 6 days ago
4
[BUG] <title>PGAP failed

#316 StickHu opened 2 weeks ago
5
[BUG] PGAP failed, docker exited with rc = 1

#315 AnmotCar closed 3 weeks ago
11
[BUG] GFF3 output file does not contain sequence-region name

#314 watsonar closed 1 month ago
3
[BUG] FATAL: "cwltool": executable file not found in $PATH in 2024-04-27.build7426

#313 komais closed 1 month ago
4
[BUG] Failing to run some sequences

#312 jmemrava closed 2 months ago
2
Species_Requirement_option

#311 cristoyerenahs closed 2 months ago
1
[BUG] PGAP fails on test genome when PGAP_INPUT_DIR set to other than default

#310 mdziurzynski closed 2 months ago
4
[BUG] Genus species requirement

#309 rsieskind closed 2 months ago
8
ORF prediction issue

#308 tangwei825 closed 2 months ago
3
PGAP for multiple users

#307 vappiah closed 3 months ago
2
source code for gc_get_molecules

#306 OH-AU closed 4 months ago
2
Error: Final process status is permanentFail

#305 sekhwal closed 3 months ago
17
Error: Final process status is permanentFail

#304 sekhwal closed 4 months ago
7
Get_Proteins_app issues

#303 asd1864714 closed 2 months ago
14
[Error] Docker exited with rc =1

#302 namho4577 closed 4 months ago
2
[Error] Docker exited with rc = 1

#301 namho4577 closed 4 months ago
3
[BUG] Final process status is permanentFail

#300 namho4577 closed 4 months ago
1
Update pgap.py

#299 iskold closed 1 month ago
3
product protein name issues

#298 asd1864714 closed 4 months ago
3
Create yeast_tat

#297 TatendaCal closed 4 months ago
0
[BUG] Fail in GenBank output file

#296 juansebe1 closed 2 months ago
9
[BUG] -c flag not received: /mnt/shared/scratch/theaven/uncompressed/hogenhout/pgap-s7

#295 TCHeaven closed 5 months ago
1
[BUG] A YAML file argument cannot be used in combination with either the -s/--organism or -g/--genome arguments

#294 TCHeaven closed 5 months ago
9
Create AcrB

#293 Ssjeela closed 5 months ago
0
pgap --update showing huge file size during installation

#292 Sabarish2001 closed 5 months ago
19
[FEATURE REQUEST] Support for Charlie Cloud Docker compatible (but more secure) container system for HPC

#291 idlfuente closed 6 months ago
1
[BUG] Failing to run my own sequence

#290 kfsb closed 5 months ago
19
[FEATURE REQUEST] Workaround for "taskset: failed to set pid 0's affinity"-Bug

#289 MrTomRod closed 6 months ago
2
[BUG] checkm dies with "OSError: AF_UNIX path too long"

#288 MrTomRod closed 5 months ago
5
[FEATURE REQUEST] Quit if no SSE4.2 support is detected

#287 MrTomRod closed 6 months ago
6
[BUG] WARNING Final process status is permanentFail

#286 snackens closed 6 months ago
9
Create EPer1

#285 Nistelrealy1988 closed 7 months ago
0
[BUG] <title>How to run pgap.py with qsub file.

#284 wurunbiao162 closed 6 months ago
5
PIPELINE TEST w/ M. genitalium - PermissionError: [Errno 13] Permission denied: '/pgap/output/debug/tmpdir

#283 raysully closed 8 months ago
38
[BUG] <title>The length of the gene exceeds the length of the conitg

#282 Moo-cow closed 6 months ago
10
[BUG] Binding non-existent file

#281 kkrick-sdsu opened 9 months ago
6
[FEATURE REQUEST] <Turn Off GO annotation>

#280 greg-harhay closed 6 months ago
7
[FEATURE REQUEST] Any plans about EGAP (Eukaryotic Genome Annotation Pipeline)?

#279 GRGong closed 9 months ago
2
Problem with running pgap annotation

#278 Subhajeet1997 closed 6 months ago
1
[FEATURE REQUEST] Unable to retrieve additional reference data from https://s3.amazonaws.com/pgap/input-[version].tgz.

#277 Tayvich closed 9 months ago
2
[BUG] PGAP analysis generates all files except .aa and .gbk

#276 Chahrazadt87 closed 6 months ago
35
Running PGAP with Metagenomic Assembled Genome

#275 kevinmyers closed 6 months ago
11
[FEATURE REQUEST] direct S3 access to input datasets

#274 jvolkening closed 8 months ago
5
[BUG] When two input genomes have same basename, the first genome is mistakenly used for the second run.

#273 pvstodghill closed 2 months ago
4
[BUG] PGAP fails install when running on singularity.

#272 Ge0rges closed 10 months ago
2
[BUG] pgap.py --update

#271 nptgiang0211 closed 6 months ago
3