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ncbi
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pgap
NCBI Prokaryotic Genome Annotation Pipeline
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[FEATURE REQUEST] Unable to retrieve additional reference data from https://s3.amazonaws.com/pgap/input-[version].tgz.
#277
Tayvich
closed
11 months ago
2
[BUG] PGAP analysis generates all files except .aa and .gbk
#276
Chahrazadt87
closed
9 months ago
35
Running PGAP with Metagenomic Assembled Genome
#275
kevinmyers
closed
8 months ago
11
[FEATURE REQUEST] direct S3 access to input datasets
#274
jvolkening
closed
10 months ago
5
[BUG] When two input genomes have same basename, the first genome is mistakenly used for the second run.
#273
pvstodghill
closed
4 months ago
4
[BUG] PGAP fails install when running on singularity.
#272
Ge0rges
closed
1 year ago
2
[BUG] pgap.py --update
#271
nptgiang0211
closed
9 months ago
3
[BUG] Podman: container name is not respected
#270
MrTomRod
closed
9 months ago
3
Failed to get rootless runtime dir
#269
tbazilegith
closed
9 months ago
2
pgap.py not found with docker container ncbi/pgap
#268
tbazilegith
closed
9 months ago
4
[FEATURE REQUEST] Add a prefix to the output files of PGAP.
#267
Dx-wmc
closed
9 months ago
2
[FEATURE REQUEST] ARM64 support
#265
rjavier17
closed
1 year ago
2
[BUG] SIGBUS error on HPC using singularity
#264
AdrianZrm
opened
1 year ago
9
[FEATURE REQUEST] Custom database for annotation
#263
zinque
closed
1 year ago
3
Advice on using PGAPs HMMs with another annotation tool
#262
tarunaaggarwal
closed
1 year ago
1
PGAP failed, docker exited with rc = 1
#261
mkapadiarch
closed
1 year ago
6
[BUG] test example failed
#260
wangdi2016
closed
1 year ago
5
Error with updating pgap
#259
stalact
closed
1 year ago
4
WARNING Final process status is permanentFail but PGAP runs fine on test data
#258
bpeacock44
closed
1 year ago
7
PGAP (2022-12-13) permanentFail
#257
adriangeerre
closed
1 year ago
15
[FEATURE REQUEST] Expected output of test_genomes?
#256
lxsteiner
closed
4 months ago
2
Help needed with Python related issues
#255
tarunaaggarwal
closed
1 year ago
7
pgap via conda
#254
tarunaaggarwal
closed
1 year ago
2
Host vs image platform issue
#253
rssherbo
closed
1 year ago
1
[BUG] dnaA truncated by PGAP gene calling
#252
tuspjo
closed
1 year ago
20
[FEATURE REQUEST] Additional check: if sequence is circular, it must also be either chromosome, plasmid, or extrachromosomal
#251
MrTomRod
closed
1 year ago
14
TaxCheck and last release
#250
tbazilegith
closed
1 year ago
2
PGAP error with my own data
#249
junkim83
closed
1 year ago
3
Error in ./pgap.py --update
#248
nbutyrate
closed
1 year ago
1
[BUG] <title>
#247
dlhuseby29
closed
1 year ago
16
Running pgap from dockerHub
#246
tbazilegith
closed
1 year ago
4
PGAP error
#245
0123615177
closed
1 year ago
109
problem with pipeline installation
#244
Khabibullin543
closed
1 year ago
1
resume a pgap run
#243
tbazilegith
closed
1 year ago
3
WARNING Final process status is permanentFail
#242
Ahmer1122
closed
1 year ago
3
[FEATURE REQUEST] Provide genome assembly/FASTA file name in ani-tax-report.txt
#241
aboffin
closed
1 year ago
1
determine the number of cores from the scheduler and not from the node
#240
vdejager
closed
1 year ago
4
WARNING Final process status is permanentFail
#239
Ahmer1122
closed
1 year ago
11
WARNING Final process status is permanentFail
#238
Ahmer1122
closed
1 year ago
0
Strategy for unknown species
#237
aboffin
closed
1 year ago
1
Issue while running on data
#236
hb660
closed
1 year ago
6
fatal error : shell /bin/sh doesn't exist in container
#235
vdejager
closed
1 year ago
7
FATAL: "cwltool": executable file not found in $PATH in 2022-12-13.build6494
#234
ponomarevsy
closed
1 year ago
6
[BUG] Error when running template
#233
cd3050
closed
1 year ago
5
Error in annotation of test genome using latest version of PGAP
#232
GanPENG-git
closed
1 year ago
2
no results
#231
kdyoung100
closed
1 year ago
2
Running the pipeline on test genome failing
#230
ac-simpson
closed
1 year ago
7
[BUG] annot.fna contents same as input FASTA file instead of CDS
#229
aboffin
closed
1 year ago
10
[FEATURE REQUEST] (a) Append "Candidatus" prefix if needed automagically. (b) Separate error from general log
#228
aboffin
closed
1 year ago
2
Error with running --taxcheck-only parameter
#226
Dx-wmc
closed
1 year ago
10
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