Error in running SpoTyping

Iam trying to run SpoTyping but am encountering this error. My input file is concatenated paired end sequences, Below us the error im getting,

File “/usr/local/tools/_conda/envs/__spotyping@2.1/bin/”, line 131

  • outlength += len(line)*
  •           ^*

SyntaxError: invalid syntax

Kindly guide me on the best way to run the TB sequences using SpoTyping.

Hi @Ngula_Monde

As a guess — that regular expression ^* is a bit odd. It means “start of a line and zero or more characters” – which translates to a non-blank line! That test is failing, which means a blank line was found. Given the framing (a calculation for the output’s line length) all of that implies an empty output, directly from the tool itself.

This is possibly some sort of sanity check the tool is running. Maybe that clue helps you to learn about what is going wrong with the inputs or settings, e.g. why no output was created. And, it is sort of a bit of a clue about the tool author’s logic – they are being “exact”. That probably means your inputs need to be exactly what is “expected”, too.

Since I’m not super familiar with this tool and don’t recognized what sub-function specifically the error message is referring to, and if you need more help, would you please share more details about the job and inputs? A shared history would be best for this. Leave everything undeleted and if you are following some tutorial, please also link that back. Troubleshooting errors

Let’s start there :slight_smile: