mlst_check

mlst_check copied to clipboard

No results from get_sequence_type

4

I download MLST database by `download_mlst_databases` and make `export MLST_DATABASES=/export/data/user/MLSTdb` ``` (base) [user@bigmem01 STRP-2020]$ get_sequence_type -a Achromobacter spp Acinetobacter baumannii 1 Acinetobacter baumannii 2 Aeromonas spp Aggregatibacter actinomycetemcomitans Anaplasma phagocytophilum...

VoronDM

Hi, I have installed mlst_check using "conda install perl-bio-mlst-check". However, I am trying to download the database, it gives an error message: Could not connect to https://pubmlst.org/data/dbases.xml Thank you, Manoj

sekhwal

Hi, i am trying to run mlst_check and i am getting this error . could you please help me out? **get_sequence_type -s "Pseudomonas aeruginosa" *.fna** Can't locate Bio/Perl.pm in @INC...

neelam19051

I used download_mlst_databases but cannot connect to https://pubmlst.org/data/dbases.xml Can I download it manually and copy into folder?

buihoangphuc412

url not found

2

MacMini:bin bgold$ ls -l total 48 -rwxr-xr-x 1 bgold staff 2413 Jan 12 01:19 download_fasta_database -rwxr-xr-x 1 bgold staff 1910 Jan 12 01:19 download_mlst_databases -rwxr-xr-x 1 bgold staff 4584 Jan...

bgold04

Hello! Thank you so much for the awesome Conda package to be able to run MLST locally. I am trying to run it on my Mac system. I created a...

chahatupreti

get_sequence_types only writes N for some fasta

2

From RT 640278: I am running get_sequence_type on a list of assemblies. It calls the STs for all, but for some fastas it only writes N as allele output, in...

ssjunnebo

Dear sanger-pathogens I'm working with mlst_check and I found this issue. The concatenates file contain DNA sequence of all alleles (glmU, pntA, sucA, tpiA, pfkB, mreA, and caiB) but the...

ghost