An error produced in scrub_sample_GFF_junctions.py about cdna_cupcake

[Magdoll]

Hi @linglingtingfei ,

Looks like the num_sample field in your file "AD_Lab.junction_detail.txt" might not be a number. Can you double check that the num_sample column looks right? If it looks fine and are all integer numbers, you may have to send me the input files for testing. You can email it to [email protected].

--Liz

[linglingtingfei]

Hi @Magdoll
Thanks for the hint, I found out the reason. There is a little problem in the "AD_Lab.junction_detail.txt" file output by summarize_sample_GFF_junctions.py. It seems there is a defect in the program. The value for the column "label" is located in other raws. I also attached a screenshot of outputs.

[bioinformatist]

Dear @Magdoll ,
I also meet this problem, and below is my "junction_detail" file contents:

It seems that the characters should be placed at "label" field came to newline in accident.
I'd like upload files needed in this step and help for reproducing this matter.
Can you help us with it?

The command I used is:

summarize_sample_GFF_junctions.py m54297_190108_070530.summarize.config m54297_190108_070530

Ahhhh... The additional file is too big for uploading. Is it convenient for providing me your email address?
Thank you in advance.

[Magdoll]

Can you update to the latest Cupcake version and first make sure the error is still reproduced?

[bioinformatist]

Yep, I'm sure that I do use the latest version of Cupcake for I just git cloned it and installed several days ago~

[bioinformatist]

@Magdoll The data used in the case is ~1 GB, I cannot upload them here.
Could you provide your email address if you're not mind?

[Magdoll]

@bioinformatist plz give me an email address and I'll send a file request

[bioinformatist]

@Magdoll My email address is [email protected], thanks~

[Magdoll]

@bioinformatist request sent

[bioinformatist]

@Magdoll Hi, I just upload files. Plz check.
I have receive URL as:
https://portal.pacificbiosciences.com/pickup.php?claimID=PgzF5cixRrM7DE4C&claimPasscode=zyK8TuSSZznX4v8r&emailAddr=etseng%40pacificbiosciences.com
And the command is summarize_sample_GFF_junctions.py m54297_190108_070530.summarize.config m54297_190108_070530

Thank you.

[bioinformatist]

@Magdoll Hi, any news about this problem?

[Magdoll]

Hi @bioinformatist ,

Apologies I was out for a while. This is now fixed and pushed to latest Cupcake version v7.0! Please give it a try.
-Liz