tseemann nullarbor issues

tseemann / nullarbor

:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology

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issues

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Update kraken2 database download link

#301 tayabsoomro opened 7 months ago
0
Can't locate Bio/SeqIO.pm in @INC

#300 claramicro opened 1 year ago
0
Gubbins

#299 Skiucabe1 opened 1 year ago
0
Custom abricate db

#298 Dangoh opened 1 year ago
0
start with assembled genomes / cgMLST

#297 shlomobl opened 2 years ago
1
Error can not read sequence

#296 akarkaba opened 2 years ago
0
How to update the MLST database

#295 safrye closed 2 years ago
1
[fai_fetch_seq] Error: fai_fetch failed.

#294 spencer411 closed 2 years ago
1
Centrifuge Issue on Install

#293 peflanag opened 2 years ago
0
make: *** [3960_Saga/sketch.msh] Error 127

#292 naikd0 opened 2 years ago
0
ERROR: Can not read reference 'NZ_CP012742.1.fna

#291 naikd0 closed 2 years ago
0
ERROR: Isolate 'PNUSAE003912-NH-M03985-170412_S13_L001' - can not read sequence #1 of 1 files: 'PNUSAE003912-NH-M03985-170412_S13_L001_R1.fq'

#290 naikd0 closed 2 years ago
0
ERROR: - can not rea' sequence #2 of 1 files

#289 spencer411 closed 2 years ago
1
error running nullarbor skesa

#288 BettyAC opened 3 years ago
3
ERROR: Could not run: snp-sites -c -o core.aln core.full.aln make: *** [Makefile:108: core.aln] Error 2

#287 emv6 closed 2 years ago
5
Report not displaying Resistome or Virulome data

#286 sdhair closed 3 years ago
1
nullarbor --check doesn't see version of shovill although shovill is installed

#285 katerinka-arh opened 3 years ago
0
no roary and report

#284 balsa012 opened 3 years ago
1
File names

#283 Dangoh opened 3 years ago
0
snps.vcf files without snp information

#282 tthye1 closed 3 years ago
1
Error installing NULLARBOR

#281 acgonzalezz opened 3 years ago
3
Set tmp folder?

#280 petroslad opened 3 years ago
0
Perl v.5.26.0 vs v.5.24.0?

#279 Michael-Sikorski opened 3 years ago
0
Error related to snippy (samtools:[faidx] Could not build fai index reference/ref.fa.fai)

#278 spencer411 closed 3 years ago
0
No report folder in OUTDIR [Makefile:108: core.aln] Error 255

#277 spencer411 closed 3 years ago
2
Acceptable phred scores?

#276 thewhittestferret closed 3 years ago
0
centrifuge database problem

#275 abdeljalil-senhaji opened 3 years ago
1
samtools --version

#274 petroslad closed 3 years ago
0
Can not read the 2nd files

#273 buihoangphuc412 closed 4 years ago
1
MakeFile:154: ref.fa.fai error 1

#272 peflanag opened 4 years ago
2
Nullarbor fails at MLST step

#271 mdiricks opened 4 years ago
0
error2 in make preview command

#270 mdiricks closed 4 years ago
1
Error: can not read sequence

#269 mdiricks closed 4 years ago
2
Deleted isolates still present in MLST table

#268 pydupont opened 4 years ago
1
Query: Mixed sample - separate reads?

#267 peflanag opened 4 years ago
2
Query: Plasmid Annotation

#266 dan-hud opened 4 years ago
0
Suggestion: Improved error messages for bad fastqs that cause problems

#265 morganx opened 4 years ago
1
ERROR: Could not find .aligned.fa/.vcf in 'file' make: *** [Makefile:108: core.aln] Error 2

#264 sharbie88 opened 4 years ago
2
minikraken2 database link needs to be updated

#263 ramay opened 4 years ago
0
Error - report not written and empty samples

#262 tristanpwdennis opened 4 years ago
1
Conda install and software versions

#261 hmontenegro opened 4 years ago
9
make again - can't find pipeline instruction file/s

#260 sharbie88 closed 4 years ago
1
Question about prefilling contigs

#259 cmkobel opened 4 years ago
7
Makefile:133 issue

#258 peflanag closed 4 years ago
6
Final report not generated and need help understanding make preview

#257 ramay closed 4 years ago
9
Kraken quibble

#256 biobrad closed 4 years ago
1
Conda installation issues

#255 emmadoughty closed 4 years ago
2
ERROR: Could not determine shovill version using '--version

#254 mabouelk closed 4 years ago
77
ERROR: Could not find .aligned.fa/.vcf in samplename make: *** [Makefile:108: core.aln] Error 2

#253 sharbie88 closed 4 years ago
6
Core.aln all the same nucleotide?

#252 foamy1881 closed 4 years ago
3