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avantonder / seqSerotyper

seqSerotyper is a tool for assigning serotypes to pneumococcal whole genome sequences
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Error in order(data.df$id) : argument 1 is not a vector Calls: [ -> [.data.frame -> order #1

Open ritma001 opened 3 years ago

ritma001 commented 3 years ago

Dear seqSerotyper team,

I recently download seqSerotyper and Run the script as suggested: Rscript seqSerotyper.R -dataFile /data/spneu/data_file.txt -srcDir /home/user/seqSerotyper/bin

However, I received an error which terminated the execution: Error in order(data.df$id) : argument 1 is not a vector Calls: [ -> [.data.frame -> order

I guess it may be due to -dataFile data_file.txt (tab delimited). So, I print out the first 3 lines as shown below: 1001123.3 /data/spneu/1001123.3.fasta 1001124.3 /data/spneu/1001124.3.fasta 1069125.3 /data/spneu/1069125.3.fasta

Do you have any idea what went wrong here? I must thank you in advance for your responses.

Best regards,

Wannisa

avantonder commented 3 years ago

Hi Wannisa,

Thanks for getting in touch. I don't support seqSerotyper anymore so I would recommend using seroba or pneumoCAT to do serotyping. That being said, did you include headers (id filePath) in your data_file.txt like the input file example in the repository?

Kind regards,

Andries