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ncbi
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pgap
NCBI Prokaryotic Genome Annotation Pipeline
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PGAP with SLURM or AWS
#172
kpenn88
closed
2 years ago
14
[Permanent Failed] WARNING [step prepare_input_template] completed permanentFail
#171
minhtrung1997
closed
2 years ago
4
PGAP failing with error "PGAP failed, docker exited with rc = 1 error" " permanentFail"
#170
Bill-Branson
closed
2 years ago
6
[BUG] Recurring permanentFail
#169
dlhuseby
closed
3 years ago
4
Unexpected results with --taxcheck-only
#168
hdore
closed
2 years ago
6
Fail to annotate a sequence construct by GATK
#167
JakeSLLeung
closed
3 years ago
8
Issue with Apple Silicon chip?
#166
Ceriz7
closed
2 years ago
17
[BUG] Failed genome annotation
#165
kevinwkeating
closed
3 years ago
5
Running pgap on a novel genus
#164
tgurbich
closed
3 years ago
14
Plastid annotation
#163
sivico26
closed
3 years ago
2
Annotation for A_baumannii_AC12 [PGAP failed, docker exited with rc = 1]
#162
wmml1234567890
closed
3 years ago
3
PGAP failed, docker exited with rc = 1
#161
Shakra-A
closed
3 years ago
5
Fails with testing dataset after fresh installation.
#160
iaconogi
closed
2 years ago
27
rundir must be determined relative to pgap.py location not '.' aka pwd
#159
EricDeveaud
closed
3 years ago
2
[FEATURE REQUEST] please set input-<VERSION>.<BUILD> loaction under environnement variable control
#158
EricDeveaud
closed
2 years ago
1
xxx_feature_table.txt file
#157
AnikaTheFox
closed
3 years ago
3
Error running test data: job Run_GeneMark_Training permanentFail
#156
eddykay310
closed
3 years ago
17
Annotation and Taxcheck fails with unknown error in release 2021-05-19.build5429: No module named '941ff00c0a6010009091__mypyc
#155
mrztm
closed
3 years ago
42
[FEATURE REQUEST] <annotation output file with nucleotide sequence >
#154
Dongho1234
closed
3 years ago
4
General question about pseudogene identification
#153
kneubehl
closed
3 years ago
1
[BUG] PGAP doesn't pull latest version of docker image (ncbi/pgap-utils:2021-05-19.build5429)
#152
rmzelle
closed
3 years ago
9
WARNING Final process status is permanent Fail
#151
Bessem06
closed
3 years ago
5
[BUG] <tmp disk space location>
#150
bowmanjeffs
closed
3 years ago
5
Install works with Internet access but not without
#149
emdyess
closed
3 years ago
2
DEBUG Copying /pgap/user_input/Rsch1.fasta to /pgap/output/Rsch1.fasta
#148
PGAPterminator
closed
3 years ago
0
DEBUG Copying /pgap/user_input/Rsch1.fasta to /pgap/output/Rsch1.fasta
#147
PGAPterminator
closed
3 years ago
6
Question
#146
anilchauhanhp9
closed
3 years ago
2
FATAL: Unable to handle docker://ncbi/pgap:2021-01-11.build5132 uri: failed to get checksum for docker://ncbi/pgap:2021-01-11.build5132:
#145
mdabalkey
closed
3 years ago
7
ent2sqn: could not find correct authors or cit-sub, resetting obligatory fields of submit-block with empty values
#144
anilchauhanhp9
closed
3 years ago
8
Prepare_Unannotated_Sequences_asnvalidate_evaluate: completed permanentFail
#143
anilchauhanhp9
closed
3 years ago
4
singularity: Error memory mapping on MG37 example data
#142
anilchauhanhp9
closed
3 years ago
4
[BUG] Installation worked but test run fails
#141
drish91
closed
3 years ago
21
Forcing use of a specific version of PGAP
#140
kneubehl
closed
3 years ago
2
[Error] Final process status is permanentFail
#139
junwkim42
closed
3 years ago
6
HTTP Error 403: rate limit exceeded
#138
ynanyam
closed
3 years ago
2
Muti-chromosome contigs
#137
vappiah
closed
3 years ago
2
Genome size check fail
#136
Biomedinformatics
closed
3 years ago
20
PGAP failed, docker exited with rc = 1, while running test genome files
#135
ankit12593
closed
3 years ago
5
errors in annotation of bacterial whole genome
#134
Biomedinformatics
closed
3 years ago
6
[BUG] Still attempting to connect to NCBI despite --no-internet flag
#133
chmaraj
closed
3 years ago
9
[BUG] PGAP fills up /tmp
#132
MrTomRod
closed
3 years ago
10
[BUG] Error installing PGAP: no space left on device
#131
Ghepardo
closed
3 years ago
7
bacterial_hit_mapping terminate called after throwing an instance of 'ncbi::CIOException'
#130
pirale
closed
3 years ago
8
pgap.cwl not found
#129
marieleoz
closed
3 years ago
10
Installation!
#128
as7a5
closed
3 years ago
10
pgap under WSL 2
#127
nclaesnacw
closed
3 years ago
4
[BUG] WARNING Final process status is permanentFail running the example test
#126
mglgc
closed
3 years ago
3
[BUG] Failure in vecscreen with no actionable message
#125
rfcohen
closed
3 years ago
14
WARNING Final process status is permanentFail[BUG] <title>
#124
vappiah
closed
3 years ago
5
APPRECIATION
#123
vappiah
closed
3 years ago
2
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