Error for the usage of parameter "-b"

[wangqi0000]

Hello,

when i use the command 1 to identify strains, command 1: strainscan -i ./E.coli-3lr.fastq -d ./strainscan/DB_Ecoli -o ./strainscan/Test/Ecoli/same-3 i got "Warning: No clusters can be detected!"

So, i use the command 2 to identify strains, which adds "-b 1" command 2: strainscan -i ./E.coli-3lr.fastq -d ./strainscan/DB_Ecoli -b 1 -o ./strainscan/Test/Ecoli/same-3 however, i got the error below:

usage: StrainScan.py [-h] -i INPUT_FQ -d DB_DIR [-o OUT_DIR] [-k KSIZE]
                     [-l LDEP] [-s MSN]
StrainScan.py: error: unrecognized arguments: -b 1

i dont't know what's wrong

Thanks for any feedback you might have!

[liaoherui]

Hi, Qi,

Thanks for using StrainScan! If you install StrainScan through Bioconda, then you can run the command below to use the latest GitHub version, which has more new features, including parameter "-b". (Note: you should run the code under the Bioconda environment you have built)

git clone https://github.com/liaoherui/StrainScan.git cd StrainScan chmod 755 library/jellyfish-linux chmod 755 library/dashing_s128 python StrainScan.py -h