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Issues list

How to update the MLST database
#295 by safrye was closed Mar 21, 2022
1
[fai_fetch_seq] Error: fai_fetch failed.
#294 by spencer411 was closed Nov 14, 2021
1
ERROR: Can not read reference 'NZ_CP012742.1.fna
#291 by naikd0 was closed Oct 28, 2021
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 by naikd0 was closed Oct 26, 2021
ERROR: - can not rea' sequence #2 of 1 files
#289 by spencer411 was closed Nov 14, 2021
1
ERROR: Could not run: snp-sites -c -o core.aln core.full.aln make: *** [Makefile:108: core.aln] Error 2
#287 by emv6 was closed Aug 23, 2021
5
Report not displaying Resistome or Virulome data
#286 by sdhair was closed Apr 20, 2021
1
snps.vcf files without snp information
#282 by tthye1 was closed Nov 24, 2020
1
Error related to snippy (samtools:[faidx] Could not build fai index reference/ref.fa.fai)
#278 by spencer411 was closed Sep 15, 2020
No report folder in OUTDIR [Makefile:108: core.aln] Error 255
#277 by spencer411 was closed Sep 11, 2020
2
Acceptable phred scores?
#276 by thewhittestferret was closed Sep 14, 2020
samtools --version
#274 by petroslad was closed Oct 22, 2020
Can not read the 2nd files user_env
#273 by buihoangphuc412 was closed Jul 17, 2020
@tseemann
1
error2 in make preview command
#270 by mdiricks was closed Jun 18, 2020
1
Error: can not read sequence help wanted
#269 by mdiricks was closed Jun 11, 2020
@tseemann
2
make again - can't find pipeline instruction file/s help wanted
#260 by sharbie88 was closed Mar 5, 2020
@tseemann
1
Makefile:133 issue help wanted
#258 by peflanag was closed Feb 26, 2020
@tseemann
6
Final report not generated and need help understanding make preview help wanted
#257 by ramay was closed Feb 26, 2020
@tseemann
9
Kraken quibble bug
#256 by biobrad was closed Feb 24, 2020
@tseemann
1
Conda installation issues help wanted packaging conda/brew
#255 by emmadoughty was closed Feb 24, 2020
@tseemann
2
ERROR: Could not determine shovill version using '--version assume_resolved help wanted
#254 by mabouelk was closed Mar 3, 2020
@tseemann
77
ERROR: Could not find .aligned.fa/.vcf in samplename make: *** [Makefile:108: core.aln] Error 2 packaging conda/brew user_env
#253 by sharbie88 was closed Feb 24, 2020
@tseemann
6
Core.aln all the same nucleotide?
#252 by foamy1881 was closed Feb 24, 2020
@tseemann
3
prokka issue [Makefile:127: M008/contigs.gff] Error 2?? user_env
#250 by foamy1881 was closed Dec 1, 2019
@tseemann
1
Making Txt file Tab for the run
#248 by foamy1881 was closed Dec 1, 2019
@tseemann
2
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