srst2

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I am trying to use getmlst.py to perform the step below for Neisseria Gonorrhoeae while following the description in the example on this repo but i get `No species matched...

Kanyerezi30

Minor fix on line 17

1

kant

Hi, I was trying to use a custom reference database with

mdiricks

VFDB Parse the cluster output and tabulate the results using the specific Virulence gene DB compatible script:

3

When I run this step: the error indicated that "File "mybin/VFDB_cdhit_to_csv.py", line 68, in sys.exit(main()) File "mybin/VFDB_cdhit_to_csv.py", line 29, in main outfile = file(args.outfile,"w") NameError: name 'file' is not defined...

aslangabriel

grep gene db syntax error

1

Hi, I have this issue at the end of running srst2 using resistance gene database. Can anyone please let me know why this error occurs and how to resolve it?...

IshwaryaMullaiSelvapandian

Please port to Python3

2

Hello, the Debian Med team is maintaining srst2 for official Debian. The recently released Debian 10 was the last Debian release featuring Python2 since this programming language is EOL. If...

tillea

list index out of range with srst2.py

3

Hello, I am trying to run the getmlst.py script. This is the command I am using: python2 /mnt/volume_2/srst2/scripts/srst2.py --input_se 669_EF_MAG_EF_MAG.fastq --output 582_mlst --log --mlst_db /mnt/volume_2/srst2/Enterococcus_faecium.fasta --mlst_definitions /mnt/volume_2/srst2/efaecium.txt --read_type q The...

anuravi1234

Meera make python3 compatible

1

Meera-Srinivasan

I came across this idea in `sistr_cmd` recently and liked it. Instead of using the input filename to guess the sample name/identifier, the user can tell you how to label...

tseemann

SRST2 installation problem with multiple Bowtie versions

1

Hi, I saw your paper and I'm really interested in what SRST2 can do. I've just installed srsts2 following the installation instructions on https://github.com/katholt/srst2. By default, install all programs in...

patms