scwatts
commented
3 years ago Hi, thanks for your interest in srst2! The error looks to be caused by a missing mlst definitions file.
I can see that PubMLST has recently updated the naming scheme for their databases (e.g. the E. coli mlst definitions file has been renamed from ecoli.txt to profiles_csv), which means the worked example is out of date.
Changing --mlst_definitions ecoli.txt to --mlst_definitions profiles_csv in the command you provided should solve this error. I've also updated the basic usage example in the README.md to reflect the changes PubMLST database naming.
Hey, I've been making my way through the worked example and I have also tried the script with my own sequences. But every time I try running the script: "srst2 --input_pe ERR024070*.fastq.gz --output shigella1 --log --save_scores --mlst_db Escherichia_coli#1.fasta --mlst_definitions ecoli.txt --gene_db ARGannot.fasta" I get an output that looks promising, but then an error message: "[Errno 2] No such file or directory: 'ecoli.txt'" I then get a "command not found" message when I try to look at any result files. I've tried everything I can find online, but each time I'm met with the same error message. I am a very new at using the command line so I know there is likely something basic that I am missing. Any advice would be great, thanks :)