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ndierckx / NOVOPlasty

NOVOPlasty - The organelle assembler and heteroplasmy caller
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Empty files but "The genome has been circularized" #148

Closed mjnetherland19 closed 4 years ago

mjnetherland19 commented 4 years ago

Hello,

After removing adapters with Trimmomatic and using a read as a seed, I was given the exact same output as you see in the log.

However, the log I have provided shows the seed as the RuBP file provided by NOVOPlasty. I did this to see if I would obtain the same output by using a seed that I knew was correct to use.

Since the problem is not with the seed, is there something that Trimmomatic is doing while removing the adapters, or could it be a problem with my reference sequence?

Also, on the topic of valid seeds, is it necessary for the seed not to be trimmed or error corrected? I would like to try and use one of my own reads again.

Here is the log file:

log_NOVOPlasty.txt

Thank you for your time.

ndierckx commented 4 years ago

Hi,

Could you run it again with extended log to 1, and send me that file?

mjnetherland19 commented 4 years ago

Unfortunately, it looks to be the same:

log_NOVOPlasty2.txt

ndierckx commented 4 years ago

yeah but that is the log file again, there should be an extended log file?

mjnetherland19 commented 4 years ago

Here it is:

log_extended_AAffAnton.txt

ndierckx commented 4 years ago

This is weird, it's the same as the normal log.. Which version you used, will test it on my laptop

mjnetherland19 commented 4 years ago

Version 4.2

It has worked for me before. I'm just now revisiting it. Not sure what I'm doing differently this time

ndierckx commented 4 years ago

I don't see how it is possible that you don't get anything in your extended log, could you redownload the NOVOPlasty and config file? You never changed anything in the code?

mjnetherland19 commented 4 years ago

I downloaded the newest version 4.2.1 and reran it Here's the extended log: log_extended_AAffAnton.txt

No, I didn't change anything in the code

ndierckx commented 4 years ago

Hi,

Sorry forgot to answer, it's because you didn't put any genome range, so it finishes the assembly immediately

mjnetherland19 commented 4 years ago

Interesting. I thought it was odd I didn't see it in the output. But it's been in my config file for every run.

I didn't mean to close this issue.

ndierckx commented 4 years ago

Can you redownload the config file and fill it in again? That usually works...

mjnetherland19 commented 4 years ago

Worked like a charm. Thanks!