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AstrobioMike / GToTree

A user-friendly workflow for phylogenomics
GNU General Public License v3.0
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Add check for input genome file not having line return after last input genome (renamed by Mike) #75

Open Calvin2077 opened 1 year ago

Calvin2077 commented 1 year ago

Hello!

I recently discovered your GToTree and have found it super helpful for my master's project and your clear instillation and instructions have been a huge help in getting it too work on my laptop so thank you very much.

I did a practice run of my species and one was dropped due to the redundancy being greater than 10%. As I am needing to include all my species for my project if there a way to increase the threshold of redundancy when using amino acids fasta files?

Thanks

AstrobioMike commented 1 year ago

Hey there, @Calvin2077!

Thanks for the kind words :)

A genome shouldn’t be dropped due to the redundancy estimate, that’s just a notice. Are you sure it’s not in the final tree? If not, it may be getting dropped for not enough target genes being found, which we can adjust

Calvin2077 commented 1 year ago

Hello AstrobioMike,

You're welcome, and thank you for getting back to me so fast it is much appreciated. And I checked my tree and I am indeed missing a species.

Moreover when I run the code "GToTree -f Untitled2.txt -o hope_new -H Archaea" it says it is only using 40 out of my 41 species despite my list (Untitled2.txt) containing all of them.

I don't know if it's related but the one that is missing is the last one on my list.

AstrobioMike commented 1 year ago

Hmm, strange. Any chance you’d be able to share the fasta files and the input Untitled.txt file with me at MikeLee\<at>bmsis.org so I can take a look? I’ll delete them right after testing of course

AstrobioMike commented 1 year ago

@Calvin2077 and i tracked down that the issue was the input file listing the paths to the genomes didn't have a line-return character at the end of the file, and the last one was being left off

i need to think about how to put in a check for this

AstrobioMike commented 1 month ago

Note for myself

I currently runn a dos2unix/cmp check on each input file, e.g.:

https://github.com/AstrobioMike/GToTree/blob/39ce5f114391938612df1df49ee6cc759208bed9/bin/GToTree#L435

I can add the --add-eol argument so they will auto-add an end-of-line to end of file if it's not there. That will address this. (Add it to the cmp checks too, so it's still only run if needed)