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christopher-vollmers / Mandalorion

Pipeline to identify isoforms from full-length cDNA sequencing data
MIT License
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have no filter isoform gtf files #2

Closed JXAUDZF closed 6 months ago

JXAUDZF commented 6 months ago

a -M APDF the result files only have a part of them.

JXAUDZF commented 6 months ago
image

install abPOA failed.

christopher-vollmers commented 6 months ago

Hi,

When did you pull your Mandalorion version? I just did some updates over the weekend and it would be helpful to know.

There might be multiple issues. It seems like the P module isn't running properly because you don't get your files converted to psl. Could you send the terminal messages from running just the -M P so I can figure out what is going on here?

The second issue is the abpoa installation. I'm not an expert on abpoa. We just pull and use it. But from quickly googling the error, it seems to be an issue with the compiler. You could either update gcc and try again or add

CFLAGS=-std=c99

to the make file and try again. If we can't figure this out, I'm sure the abpoa people can help.

Best, Chris

JXAUDZF commented 6 months ago
image

and the software abPOA is installed fail contribute to the results,I don't know how to make successfully.

JXAUDZF commented 6 months ago

have been soluted.Thank you.

JXAUDZF commented 6 months ago
image

have no gif file

JXAUDZF commented 6 months ago
image

seem P mole is error

JXAUDZF commented 6 months ago

Thanks for soluting the questions!

christopher-vollmers commented 6 months ago

Hi,

the error in P is just a warning. I does break anything so it should be fine.

Do you still have no gtf? It's not clear right now where things are breaking or if they are still breaking.

Best, Chris

JXAUDZF commented 6 months ago

have succeeded, thank you very much.